/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.masked /home/seqanal//RepeatMasker20020713/Libraries/is.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/identity.matrix -minmatch 15 -minscore 17 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180000
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ...1.008 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.654 Mbytes in 4 blocks
Complementing ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.654 Mbytes in 4 blocks
Allocating align_entries ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.379 Mbytes in 4 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 1.512 Mbytes; currently free: 0.379 Mbytes in 4 blocks
4.536 Mbytes allocated -- total 6.048 Mbytes
Finding words ...
 0  723724
 10  323265
 20  972
 30  297
 40  130
 50  48
 60  56
 70  54
 80  6
 90  6
 100  4
 110  6
 130  3
 140  2
 150  1
 680  2
min no. words: 0 at 22
max no. words: 677 at 0
avg no. words: 0.02.520 Mbytes allocated -- total 8.568 Mbytes
1.008 Mbytes allocated -- total 9.576 Mbytes
 Done
Total space allocated: 9.576 Mbytes; currently free: 1.445 Mbytes in 7 blocks
550000 words; after pruning: 549972
Sorting words ... Done

15  516170
Finding subject matches ... Done
Total space allocated: 9.576 Mbytes; currently free: 1.448 Mbytes in 7 blocks
# pass words: 0, #fail words: 4
Quickalign: 0 successes, 0 failures
0 SWAT alignments performed. 0 pairs have score >= 17
Making reversed pairs ... Done
Total space allocated: 9.576 Mbytes; currently free: 8.392 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 9.576 Mbytes; currently free: 8.392 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 9.576 Mbytes; currently free: 8.392 Mbytes in 7 blocks
Total space allocated: 9.576 Mbytes; currently free: 8.392 Mbytes in 7 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180000
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  968033
 10  80507
 20  32
 50  1
 60  1
 120  2
min no. words: 0 at 4
max no. words: 116 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.606 Mbytes in 4 blocks
93668 words; after pruning: 93650
Sorting words ... Done

10  80543
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
1.008 Mbytes allocated -- total 7.560 Mbytes
.... Done
Total space allocated: 7.560 Mbytes; currently free: 1.776 Mbytes in 9 blocks
# pass words: 8622, #fail words: 0
Quickalign: 229 successes, 0 failures
4691 SWAT alignments performed. 229 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.434 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.186 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.187 Mbytes in 10 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.187 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1695, in 229 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p47g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180000
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  968341
 10  80203
 20  30
 120  2
min no. words: 0 at 4
max no. words: 116 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.610 Mbytes in 4 blocks
93196 words; after pruning: 93058
Sorting words ... Done

10  80235
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
.
descrip_buffer expanded1.008 Mbytes allocated -- total 7.560 Mbytes
 Done
Total space allocated: 7.560 Mbytes; currently free: 1.782 Mbytes in 9 blocks
# pass words: 2862, #fail words: 10766
Quickalign: 247 successes, 18 failures
1705 SWAT alignments performed. 265 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.425 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.178 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.179 Mbytes in 10 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.179 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 13496, in 265 lists, size: 0.013 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p47g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180000
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.335 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.335 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.293 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.293 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  972539
 10  76035
 30  2
min no. words: 0 at 4
max no. words: 22 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.161 Mbytes in 3 blocks
84904 words; after pruning: 84504
Sorting words ... Done

10  76037
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded1.008 Mbytes allocated -- total 7.056 Mbytes
 Done
Total space allocated: 7.056 Mbytes; currently free: 1.668 Mbytes in 9 blocks
# pass words: 524, #fail words: 3560
Quickalign: 0 successes, 0 failures
460 SWAT alignments performed. 0 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 6.285 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 7.056 Mbytes; currently free: 6.285 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 6.285 Mbytes in 8 blocks
Total space allocated: 7.056 Mbytes; currently free: 6.285 Mbytes in 8 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p47g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180001
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.335 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.335 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.293 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.293 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  972570
 10  76004
 30  2
min no. words: 0 at 4
max no. words: 22 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.162 Mbytes in 3 blocks
84904 words; after pruning: 84464
Sorting words ... Done

11  81296
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes
1.008 Mbytes allocated -- total 8.064 Mbytes
.. Done
Total space allocated: 8.064 Mbytes; currently free: 2.399 Mbytes in 9 blocks
# pass words: 2877, #fail words: 6629
Quickalign: 65 successes, 87 failures
2932 SWAT alignments performed. 144 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 8.064 Mbytes; currently free: 7.002 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 8.064 Mbytes; currently free: 6.772 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 8.064 Mbytes; currently free: 6.773 Mbytes in 10 blocks
Total space allocated: 8.064 Mbytes; currently free: 6.773 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 11406, in 144 lists, size: 0.011 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p47g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180003
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  978936
 10  69638
 20  2
min no. words: 0 at 4
max no. words: 19 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.213 Mbytes in 3 blocks
77250 words; after pruning: 76590
Sorting words ... Done

11  74058
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.991 Mbytes in 8 blocks
# pass words: 972, #fail words: 1596
Quickalign: 22 successes, 44 failures
611 SWAT alignments performed. 61 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.558 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.343 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.343 Mbytes in 7 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.343 Mbytes in 7 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 9977, in 61 lists, size: 0.010 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p47g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180004
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  981257
 10  67317
 20  2
min no. words: 0 at 4
max no. words: 19 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.230 Mbytes in 3 blocks
74524 words; after pruning: 73884
Sorting words ... Done

10  67319
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.048 Mbytes; currently free: 0.534 Mbytes in 8 blocks
# pass words: 382, #fail words: 2917
Quickalign: 17 successes, 1 failures
394 SWAT alignments performed. 14 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.097 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.888 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.888 Mbytes in 8 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.888 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 387, in 14 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p47g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180004
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  206348
 10  55792
 20  4
min no. words: 0 at 6
max no. words: 16 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.353 Mbytes in 3 blocks
74524 words; after pruning: 73656
Sorting words ... Done

9  55796
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes

descrip_buffer expanded. Done
Total space allocated: 3.024 Mbytes; currently free: 0.914 Mbytes in 8 blocks
# pass words: 1146, #fail words: 5029
Quickalign: 0 successes, 0 failures
1121 SWAT alignments performed. 0 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.331 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 3.024 Mbytes; currently free: 2.331 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.331 Mbytes in 7 blocks
Total space allocated: 3.024 Mbytes; currently free: 2.331 Mbytes in 7 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p47g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180005
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  981479
 10  67095
 20  2
min no. words: 0 at 4
max no. words: 11 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.232 Mbytes in 3 blocks
74524 words; after pruning: 73592
Sorting words ... Done

10  67097
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded.0.504 Mbytes allocated -- total 6.552 Mbytes
....... Done
Total space allocated: 6.552 Mbytes; currently free: 1.029 Mbytes in 10 blocks
# pass words: 9704, #fail words: 20571
Quickalign: 15 successes, 24 failures
9578 SWAT alignments performed. 36 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.588 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.379 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.379 Mbytes in 10 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.379 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2015, in 36 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p47g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180009
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  985367
 10  63207
 20  2
min no. words: 0 at 4
max no. words: 11 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.254 Mbytes in 3 blocks
74524 words; after pruning: 69060
Sorting words ... Done

10  63209
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
....
descrip_buffer expanded. Done
Total space allocated: 6.552 Mbytes; currently free: 1.047 Mbytes in 10 blocks
# pass words: 5124, #fail words: 11579
Quickalign: 5 successes, 65 failures
5034 SWAT alignments performed. 52 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.579 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.369 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.369 Mbytes in 9 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.369 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 7543, in 52 lists, size: 0.008 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p47g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180013
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  35899
 10  29622
 20  13
 30  2
min no. words: 0 at 17
max no. words: 23 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.216 Mbytes in 3 blocks
74524 words; after pruning: 56666
Sorting words ... Done

8  29637
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
.. Done
Total space allocated: 2.520 Mbytes; currently free: 1.017 Mbytes in 8 blocks
# pass words: 2788, #fail words: 5268
Quickalign: 12 successes, 48 failures
2220 SWAT alignments performed. 42 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.559 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.358 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.358 Mbytes in 10 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.358 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2560, in 42 lists, size: 0.003 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p47g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180014
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  38443
 10  27088
 20  3
 30  2
min no. words: 0 at 17
max no. words: 23 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.258 Mbytes in 3 blocks
74524 words; after pruning: 48382
Sorting words ... Done

8  27093
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.819 Mbytes in 6 blocks
# pass words: 157, #fail words: 233
Quickalign: 0 successes, 0 failures
152 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.323 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 2.016 Mbytes; currently free: 1.323 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.323 Mbytes in 5 blocks
Total space allocated: 2.016 Mbytes; currently free: 1.323 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p47g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180014
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  1003876
 10  44698
 20  2
min no. words: 0 at 3
max no. words: 11 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.359 Mbytes in 3 blocks
74524 words; after pruning: 48046
Sorting words ... Done

11  46656
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
... Done
Total space allocated: 6.048 Mbytes; currently free: 0.920 Mbytes in 6 blocks
# pass words: 3127, #fail words: 6235
Quickalign: 0 successes, 0 failures
3065 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.355 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 5.355 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.355 Mbytes in 5 blocks
Total space allocated: 6.048 Mbytes; currently free: 5.355 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p47g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180021
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  222824
 10  39318
 20  2
min no. words: 0 at 6
max no. words: 15 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.480 Mbytes in 3 blocks
74524 words; after pruning: 48270
Sorting words ... Done

9  39320
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
... Done
Total space allocated: 3.024 Mbytes; currently free: 0.775 Mbytes in 7 blocks
# pass words: 4309, #fail words: 11067
Quickalign: 0 successes, 5 failures
3998 SWAT alignments performed. 5 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.064 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.359 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.359 Mbytes in 8 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.359 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 967, in 5 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180024
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  224124
 10  38018
 20  2
min no. words: 0 at 6
max no. words: 15 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.489 Mbytes in 3 blocks
74524 words; after pruning: 46464
Sorting words ... Done

9  38020
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
 Done
Total space allocated: 2.520 Mbytes; currently free: 0.552 Mbytes in 5 blocks
# pass words: 9483, #fail words: 0
Quickalign: 0 successes, 0 failures
258 SWAT alignments performed. 0 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.833 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 2.520 Mbytes; currently free: 1.833 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.833 Mbytes in 4 blocks
Total space allocated: 2.520 Mbytes; currently free: 1.833 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180024
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  39080
 10  26452
 20  2
 30  2
min no. words: 0 at 14
max no. words: 23 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.267 Mbytes in 3 blocks
74524 words; after pruning: 46576
Sorting words ... Done

8  26456
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.571 Mbytes in 7 blocks
# pass words: 26675, #fail words: 0
Quickalign: 3 successes, 0 failures
742 SWAT alignments performed. 3 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.066 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.369 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.369 Mbytes in 10 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.369 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 48, in 3 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180024
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.346 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment1.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.308 Mbytes in 2 blocks
Finding words ...
 0  6
 10  166
 20  90
 30  90
 40  136
 50  118
 60  132
 70  78
 80  66
 90  44
 100  24
 110  34
 120  16
 130  10
 140  8
 160  6
min no. words: 0 at 396
max no. words: 157 at 338
avg no. words: 0.0 Done
Total space allocated: 0.504 Mbytes; currently free: 0.019 Mbytes in 2 blocks
74524 words; after pruning: 46802
Sorting words ... Done

5  1018
Finding subject matches ...0.504 Mbytes allocated -- total 1.008 Mbytes
0.504 Mbytes allocated -- total 1.512 Mbytes
.0.504 Mbytes allocated -- total 2.016 Mbytes
.. Done
Total space allocated: 2.016 Mbytes; currently free: 1.085 Mbytes in 6 blocks
# pass words: 17272, #fail words: 0
Quickalign: 0 successes, 0 failures
3089 SWAT alignments performed. 0 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.323 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 2.016 Mbytes; currently free: 1.323 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.323 Mbytes in 5 blocks
Total space allocated: 2.016 Mbytes; currently free: 1.323 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180025
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  967542
 10  80992
 20  12
 30  4
 40  6
 50  8
 60  10
 80  2
min no. words: 0 at 4
max no. words: 77 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.606 Mbytes in 4 blocks
93668 words; after pruning: 93650
Sorting words ... Done

10  81034
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes
....1.008 Mbytes allocated -- total 8.064 Mbytes
. Done
Total space allocated: 8.064 Mbytes; currently free: 2.280 Mbytes in 8 blocks
# pass words: 9919, #fail words: 0
Quickalign: 275 successes, 8 failures
5503 SWAT alignments performed. 283 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 8.064 Mbytes; currently free: 6.934 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 8.064 Mbytes; currently free: 6.685 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 8.064 Mbytes; currently free: 6.686 Mbytes in 10 blocks
Total space allocated: 8.064 Mbytes; currently free: 6.686 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 5166, in 283 lists, size: 0.005 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p45g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180025
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  967718
 10  80824
 20  8
 30  4
 40  6
 50  6
 60  8
 80  2
min no. words: 0 at 4
max no. words: 77 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.609 Mbytes in 4 blocks
93304 words; after pruning: 93166
Sorting words ... Done

10  80858
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes

descrip_buffer expanded1.008 Mbytes allocated -- total 7.560 Mbytes
 Done
Total space allocated: 7.560 Mbytes; currently free: 1.781 Mbytes in 9 blocks
# pass words: 1397, #fail words: 7621
Quickalign: 94 successes, 19 failures
902 SWAT alignments performed. 113 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.433 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.186 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.187 Mbytes in 10 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.187 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 6449, in 113 lists, size: 0.006 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p45g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180025
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.331 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.331 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.286 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.286 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  969972
 10  78570
 20  8
 30  6
 40  6
 50  6
 60  8
min no. words: 0 at 4
max no. words: 55 at 835788
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.634 Mbytes in 4 blocks
89666 words; after pruning: 89408
Sorting words ... Done

10  78604
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes

descrip_buffer expanded Done
Total space allocated: 7.056 Mbytes; currently free: 1.608 Mbytes in 7 blocks
# pass words: 409, #fail words: 3797
Quickalign: 0 successes, 0 failures
380 SWAT alignments performed. 0 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 6.249 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 7.056 Mbytes; currently free: 6.249 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 6.249 Mbytes in 8 blocks
Total space allocated: 7.056 Mbytes; currently free: 6.249 Mbytes in 8 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p45g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180025
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.331 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.331 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.286 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.286 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  969993
 10  78549
 20  8
 30  6
 40  6
 50  6
 60  8
min no. words: 0 at 4
max no. words: 55 at 835788
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.634 Mbytes in 4 blocks
89666 words; after pruning: 89382
Sorting words ... Done

11  84502
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
.. Done
Total space allocated: 6.552 Mbytes; currently free: 0.823 Mbytes in 7 blocks
# pass words: 2656, #fail words: 7525
Quickalign: 22 successes, 29 failures
2655 SWAT alignments performed. 47 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.461 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.221 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.222 Mbytes in 8 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.222 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 3195, in 47 lists, size: 0.003 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p45g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180028
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.332 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.332 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.288 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.288 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  971479
 10  77063
 20  10
 30  4
 40  6
 50  6
 60  8
min no. words: 0 at 4
max no. words: 55 at 835788
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.646 Mbytes in 4 blocks
87886 words; after pruning: 87536
Sorting words ... Done

11  82798
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
1.008 Mbytes allocated -- total 7.560 Mbytes
 Done
Total space allocated: 7.560 Mbytes; currently free: 1.849 Mbytes in 8 blocks
# pass words: 1627, #fail words: 2361
Quickalign: 24 successes, 101 failures
872 SWAT alignments performed. 125 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.457 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.221 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.221 Mbytes in 9 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.221 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 22594, in 125 lists, size: 0.023 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p45g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180029
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  971752
 10  76790
 20  10
 30  4
 40  6
 50  6
 60  8
min no. words: 0 at 4
max no. words: 55 at 835788
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.648 Mbytes in 4 blocks
87548 words; after pruning: 87210
Sorting words ... Done

10  76824
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes

descrip_buffer expanded Done
Total space allocated: 7.056 Mbytes; currently free: 1.635 Mbytes in 7 blocks
# pass words: 299, #fail words: 2562
Quickalign: 0 successes, 0 failures
294 SWAT alignments performed. 0 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 6.265 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 7.056 Mbytes; currently free: 6.265 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 6.265 Mbytes in 8 blocks
Total space allocated: 7.056 Mbytes; currently free: 6.265 Mbytes in 8 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180029
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  199870
 10  62228
 20  22
 30  2
 40  2
 50  6
 60  8
 70  6
min no. words: 0 at 4
max no. words: 67 at 52416
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.265 Mbytes in 3 blocks
87548 words; after pruning: 87244
Sorting words ... Done

9  62274
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
1.008 Mbytes allocated -- total 3.528 Mbytes

descrip_buffer expanded. Done
Total space allocated: 3.528 Mbytes; currently free: 1.252 Mbytes in 7 blocks
# pass words: 1254, #fail words: 5814
Quickalign: 0 successes, 0 failures
1219 SWAT alignments performed. 0 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.737 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 3.528 Mbytes; currently free: 2.737 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.737 Mbytes in 6 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.737 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180029
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  971752
 10  76790
 20  10
 30  4
 40  6
 50  6
 60  8
min no. words: 0 at 4
max no. words: 55 at 835788
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.648 Mbytes in 4 blocks
87548 words; after pruning: 87210
Sorting words ... Done

10  76824
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded......... Done
Total space allocated: 7.056 Mbytes; currently free: 1.351 Mbytes in 9 blocks
# pass words: 10784, #fail words: 27448
Quickalign: 15 successes, 19 failures
10625 SWAT alignments performed. 24 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.980 Mbytes in 10 blocks
Printing matches ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.745 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.745 Mbytes in 10 blocks
Total space allocated: 7.056 Mbytes; currently free: 5.745 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1543, in 24 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180034
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  974346
 10  74196
 20  10
 30  4
 40  6
 50  6
 60  8
min no. words: 0 at 4
max no. words: 55 at 835788
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.159 Mbytes in 3 blocks
87548 words; after pruning: 84142
Sorting words ... Done

10  74230
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
1.008 Mbytes allocated -- total 6.552 Mbytes
0.504 Mbytes allocated -- total 7.056 Mbytes
.....
descrip_buffer expanded. Done
Total space allocated: 7.056 Mbytes; currently free: 1.358 Mbytes in 9 blocks
# pass words: 7487, #fail words: 17283
Quickalign: 42 successes, 206 failures
6238 SWAT alignments performed. 226 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.933 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.697 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.698 Mbytes in 10 blocks
Total space allocated: 7.056 Mbytes; currently free: 5.698 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 37998, in 226 lists, size: 0.038 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p45g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180039
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  37221
 10  28251
 20  44
 30  2
 60  8
 70  4
 80  2
 90  2
 100  1
 120  1
min no. words: 0 at 6
max no. words: 112 at 52428
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.208 Mbytes in 3 blocks
87548 words; after pruning: 54426
Sorting words ... Done

8  28315
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
1.008 Mbytes allocated -- total 2.520 Mbytes
.. Done
Total space allocated: 2.520 Mbytes; currently free: 0.911 Mbytes in 6 blocks
# pass words: 2623, #fail words: 5215
Quickalign: 23 successes, 32 failures
2113 SWAT alignments performed. 45 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.442 Mbytes in 5 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
0.504 Mbytes allocated -- total 4.536 Mbytes
 Done
Total space allocated: 4.536 Mbytes; currently free: 3.223 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 4.536 Mbytes; currently free: 3.223 Mbytes in 10 blocks
Total space allocated: 4.536 Mbytes; currently free: 3.223 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1952, in 45 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p45g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180040
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  39899
 10  25583
 20  36
 60  8
 70  4
 80  2
 90  2
 100  1
 120  1
min no. words: 0 at 6
max no. words: 112 at 52428
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.247 Mbytes in 3 blocks
87548 words; after pruning: 46604
Sorting words ... Done

8  25637
Finding subject matches ...1.008 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.741 Mbytes in 5 blocks
# pass words: 157, #fail words: 240
Quickalign: 0 successes, 0 failures
149 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.236 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 2.016 Mbytes; currently free: 1.236 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.236 Mbytes in 4 blocks
Total space allocated: 2.016 Mbytes; currently free: 1.236 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180040
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  1007017
 10  41526
 20  9
 30  4
 40  6
 50  6
 60  8
min no. words: 0 at 1
max no. words: 54 at 197427
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.348 Mbytes in 3 blocks
87548 words; after pruning: 46338
Sorting words ... Done

11  43574
Finding subject matches ...1.008 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes
.. Done
Total space allocated: 7.056 Mbytes; currently free: 1.680 Mbytes in 6 blocks
# pass words: 2755, #fail words: 6616
Quickalign: 2 successes, 2 failures
2724 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 6.107 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 7.056 Mbytes; currently free: 6.107 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 6.107 Mbytes in 6 blocks
Total space allocated: 7.056 Mbytes; currently free: 6.107 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p45g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180046
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  225650
 10  36454
 20  18
 30  2
 50  6
 60  10
 70  4
min no. words: 0 at 4
max no. words: 65 at 52416
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.469 Mbytes in 3 blocks
87548 words; after pruning: 46514
Sorting words ... Done

9  36494
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
1.008 Mbytes allocated -- total 3.528 Mbytes
... Done
Total space allocated: 3.528 Mbytes; currently free: 1.169 Mbytes in 7 blocks
# pass words: 3822, #fail words: 14279
Quickalign: 1 successes, 6 failures
3571 SWAT alignments performed. 7 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.449 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 4.032 Mbytes
0.504 Mbytes allocated -- total 4.536 Mbytes
 Done
Total space allocated: 4.536 Mbytes; currently free: 3.221 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 4.536 Mbytes; currently free: 3.222 Mbytes in 8 blocks
Total space allocated: 4.536 Mbytes; currently free: 3.222 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1968, in 7 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180049
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  226308
 10  35828
 20  8
min no. words: 0 at 4
max no. words: 16 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.482 Mbytes in 3 blocks
87548 words; after pruning: 43876
Sorting words ... Done

9  35836
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
1.008 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 1.193 Mbytes in 8 blocks
# pass words: 10227, #fail words: 0
Quickalign: 4 successes, 2 failures
291 SWAT alignments performed. 6 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.461 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 4.032 Mbytes
0.504 Mbytes allocated -- total 4.536 Mbytes
 Done
Total space allocated: 4.536 Mbytes; currently free: 3.234 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 4.536 Mbytes; currently free: 3.234 Mbytes in 10 blocks
Total space allocated: 4.536 Mbytes; currently free: 3.234 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 114, in 6 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180049
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  40399
 10  25121
 20  16
min no. words: 0 at 6
max no. words: 17 at 17893
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.263 Mbytes in 3 blocks
87548 words; after pruning: 43442
Sorting words ... Done

8  25137
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
1.008 Mbytes allocated -- total 3.024 Mbytes
 Done
Total space allocated: 3.024 Mbytes; currently free: 1.478 Mbytes in 8 blocks
# pass words: 25876, #fail words: 0
Quickalign: 5 successes, 1 failures
745 SWAT alignments performed. 6 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 1.957 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
0.504 Mbytes allocated -- total 4.536 Mbytes
 Done
Total space allocated: 4.536 Mbytes; currently free: 3.234 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 4.536 Mbytes; currently free: 3.234 Mbytes in 11 blocks
Total space allocated: 4.536 Mbytes; currently free: 3.234 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 324, in 6 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180049
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.333 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment2.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.289 Mbytes in 2 blocks
Finding words ...
 0  4
 10  188
 20  90
 30  136
 40  110
 50  166
 60  82
 70  74
 80  52
 90  32
 100  44
 110  18
 120  12
 130  6
 140  4
 150  2
 160  4
min no. words: 0 at 102
max no. words: 157 at 330
avg no. words: 0.0 Done
Total space allocated: 0.504 Mbytes; currently free: 0.019 Mbytes in 2 blocks
87548 words; after pruning: 42986
Sorting words ... Done

5  1020
Finding subject matches ...0.504 Mbytes allocated -- total 1.008 Mbytes
1.008 Mbytes allocated -- total 2.016 Mbytes
... Done
Total space allocated: 2.016 Mbytes; currently free: 1.006 Mbytes in 5 blocks
# pass words: 15020, #fail words: 0
Quickalign: 0 successes, 0 failures
3240 SWAT alignments performed. 0 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.225 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 2.016 Mbytes; currently free: 1.225 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.225 Mbytes in 4 blocks
Total space allocated: 2.016 Mbytes; currently free: 1.225 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180050
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  970948
 10  77514
 20  108
 30  4
 100  2
min no. words: 0 at 6
max no. words: 93 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.606 Mbytes in 4 blocks
93668 words; after pruning: 93650
Sorting words ... Done

10  77628
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes
....... Done
Total space allocated: 7.056 Mbytes; currently free: 1.275 Mbytes in 7 blocks
# pass words: 11123, #fail words: 0
Quickalign: 524 successes, 4 failures
7268 SWAT alignments performed. 528 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.879 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.629 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.631 Mbytes in 9 blocks
Total space allocated: 7.056 Mbytes; currently free: 5.631 Mbytes in 9 blocks
Total # pairs: 2000, size: 0.088 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 8206, in 528 lists, size: 0.008 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p49g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180050
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  971128
 10  77346
 20  100
 100  2
min no. words: 0 at 6
max no. words: 93 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.609 Mbytes in 4 blocks
93288 words; after pruning: 93150
Sorting words ... Done

10  77448
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
1.008 Mbytes allocated -- total 7.560 Mbytes
.
descrip_buffer expanded. Done
Total space allocated: 7.560 Mbytes; currently free: 1.781 Mbytes in 10 blocks
# pass words: 4019, #fail words: 10553
Quickalign: 317 successes, 50 failures
2169 SWAT alignments performed. 362 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.418 Mbytes in 11 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.170 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.172 Mbytes in 11 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.172 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 18725, in 362 lists, size: 0.019 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p49g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180050
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.339 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.339 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.298 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.298 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  976978
 10  71592
 20  4
 30  2
min no. words: 0 at 4
max no. words: 21 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.185 Mbytes in 3 blocks
81328 words; after pruning: 80840
Sorting words ... Done

10  71598
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes

descrip_buffer expanded Done
Total space allocated: 5.544 Mbytes; currently free: 0.201 Mbytes in 6 blocks
# pass words: 578, #fail words: 3238
Quickalign: 0 successes, 0 failures
483 SWAT alignments performed. 0 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 5.544 Mbytes; currently free: 4.800 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 5.544 Mbytes; currently free: 4.800 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 5.544 Mbytes; currently free: 4.800 Mbytes in 6 blocks
Total space allocated: 5.544 Mbytes; currently free: 4.800 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p49g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180051
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.339 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.339 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.298 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.298 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  977016
 10  71554
 20  4
 30  2
min no. words: 0 at 4
max no. words: 21 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.185 Mbytes in 3 blocks
81328 words; after pruning: 80792
Sorting words ... Done

11  76870
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.. Done
Total space allocated: 6.048 Mbytes; currently free: 0.433 Mbytes in 7 blocks
# pass words: 2931, #fail words: 6846
Quickalign: 54 successes, 71 failures
2904 SWAT alignments performed. 121 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.021 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.798 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.799 Mbytes in 8 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.799 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 9015, in 121 lists, size: 0.009 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p49g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180053
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  980159
 10  68411
 20  4
 30  2
min no. words: 0 at 4
max no. words: 21 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.209 Mbytes in 3 blocks
77662 words; after pruning: 77082
Sorting words ... Done

11  73356
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.985 Mbytes in 8 blocks
# pass words: 532, #fail words: 1354
Quickalign: 19 successes, 36 failures
531 SWAT alignments performed. 46 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.560 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.345 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.345 Mbytes in 8 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.345 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 4245, in 46 lists, size: 0.004 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p49g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180054
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  980116
 10  68454
 20  4
 30  2
min no. words: 0 at 4
max no. words: 21 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.209 Mbytes in 3 blocks
77662 words; after pruning: 77134
Sorting words ... Done

10  68460
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.994 Mbytes in 10 blocks
# pass words: 568, #fail words: 3214
Quickalign: 0 successes, 4 failures
481 SWAT alignments performed. 2 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.574 Mbytes in 10 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.358 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.358 Mbytes in 11 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.358 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 81, in 2 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p49g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180054
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  206076
 10  56046
 20  20
 30  2
min no. words: 0 at 6
max no. words: 28 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.333 Mbytes in 3 blocks
77662 words; after pruning: 76784
Sorting words ... Done

9  56068
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes

descrip_buffer expanded. Done
Total space allocated: 3.528 Mbytes; currently free: 1.114 Mbytes in 10 blocks
# pass words: 1382, #fail words: 7001
Quickalign: 22 successes, 21 failures
1357 SWAT alignments performed. 43 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.544 Mbytes in 10 blocks
Printing matches ... 0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.833 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.833 Mbytes in 11 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.833 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1631, in 43 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p49g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180054
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  980845
 10  67725
 20  4
 30  2
min no. words: 0 at 4
max no. words: 21 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.214 Mbytes in 3 blocks
77662 words; after pruning: 76182
Sorting words ... Done

10  67731
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded........ Done
Total space allocated: 6.048 Mbytes; currently free: 0.490 Mbytes in 8 blocks
# pass words: 10120, #fail words: 23170
Quickalign: 26 successes, 34 failures
9975 SWAT alignments performed. 54 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.061 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.846 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.846 Mbytes in 9 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.846 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 3158, in 54 lists, size: 0.003 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p49g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180059
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  984326
 10  64244
 20  4
 30  2
min no. words: 0 at 4
max no. words: 21 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.236 Mbytes in 3 blocks
77662 words; after pruning: 71766
Sorting words ... Done

10  64250
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
...
descrip_buffer expanded. Done
Total space allocated: 6.552 Mbytes; currently free: 1.005 Mbytes in 11 blocks
# pass words: 4906, #fail words: 13110
Quickalign: 17 successes, 67 failures
4804 SWAT alignments performed. 79 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.551 Mbytes in 10 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.336 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.336 Mbytes in 10 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.336 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 6190, in 79 lists, size: 0.006 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p49g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180102
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  33982
 10  31381
 20  161
 30  10
 40  2
min no. words: 0 at 4
max no. words: 33 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.667 Mbytes in 4 blocks
77662 words; after pruning: 66374
Sorting words ... Done

8  31554
Finding subject matches ...0.504 Mbytes allocated -- total 2.016 Mbytes
.. Done
Total space allocated: 2.016 Mbytes; currently free: 0.440 Mbytes in 5 blocks
# pass words: 3032, #fail words: 6820
Quickalign: 22 successes, 26 failures
2463 SWAT alignments performed. 39 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.032 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.833 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.833 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.833 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1570, in 39 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p49g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180104
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  35696
 10  29697
 20  131
 30  10
 40  2
min no. words: 0 at 4
max no. words: 33 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.192 Mbytes in 3 blocks
77662 words; after pruning: 60556
Sorting words ... Done

8  29840
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.738 Mbytes in 6 blocks
# pass words: 226, #fail words: 353
Quickalign: 0 successes, 0 failures
217 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.303 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 2.016 Mbytes; currently free: 1.303 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.303 Mbytes in 5 blocks
Total space allocated: 2.016 Mbytes; currently free: 1.303 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p49g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180104
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  994439
 10  54131
 20  6
min no. words: 0 at 4
max no. words: 19 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.294 Mbytes in 3 blocks
77662 words; after pruning: 60226
Sorting words ... Done

11  57552
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
... Done
Total space allocated: 6.552 Mbytes; currently free: 1.197 Mbytes in 8 blocks
# pass words: 3643, #fail words: 8800
Quickalign: 1 successes, 1 failures
3582 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.693 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.693 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.693 Mbytes in 7 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.693 Mbytes in 7 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p49g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180112
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  216382
 10  45742
 20  18
 30  2
min no. words: 0 at 4
max no. words: 24 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.414 Mbytes in 3 blocks
77662 words; after pruning: 60446
Sorting words ... Done

9  45762
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
.0.504 Mbytes allocated -- total 3.024 Mbytes
... Done
Total space allocated: 3.024 Mbytes; currently free: 0.688 Mbytes in 7 blocks
# pass words: 4928, #fail words: 14343
Quickalign: 0 successes, 4 failures
4608 SWAT alignments performed. 4 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.039 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.831 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.831 Mbytes in 9 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.831 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 308, in 4 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180115
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  217102
 10  45022
 20  18
 30  2
min no. words: 0 at 4
max no. words: 24 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.419 Mbytes in 3 blocks
77662 words; after pruning: 59426
Sorting words ... Done

9  45042
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 1.207 Mbytes in 9 blocks
# pass words: 14995, #fail words: 0
Quickalign: 11 successes, 9 failures
432 SWAT alignments performed. 20 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.552 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 3.528 Mbytes; currently free: 2.336 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.337 Mbytes in 9 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.337 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 743, in 20 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180116
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  36173
 10  29294
 20  67
 40  2
min no. words: 0 at 4
max no. words: 33 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.205 Mbytes in 3 blocks
77662 words; after pruning: 57936
Sorting words ... Done

8  29363
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
. Done
Total space allocated: 2.016 Mbytes; currently free: 0.486 Mbytes in 7 blocks
# pass words: 36942, #fail words: 0
Quickalign: 3 successes, 2 failures
1114 SWAT alignments performed. 5 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.038 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.839 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.839 Mbytes in 11 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.839 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 125, in 5 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180116
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment3.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Finding words ...
 10  132
 20  88
 30  82
 40  122
 50  112
 60  106
 70  96
 80  50
 90  42
 100  30
 110  44
 120  20
 130  26
 140  16
 150  14
 160  22
 170  6
 180  2
 190  6
 200  4
 210  4
min no. words: 2 at 102
max no. words: 203 at 330
avg no. words: 0.00.504 Mbytes allocated -- total 1.008 Mbytes
 Done
Total space allocated: 1.008 Mbytes; currently free: 0.463 Mbytes in 3 blocks
77662 words; after pruning: 57790
Sorting words ... Done

5  1024
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
.... Done
Total space allocated: 2.016 Mbytes; currently free: 0.745 Mbytes in 8 blocks
# pass words: 22980, #fail words: 0
Quickalign: 16 successes, 0 failures
4229 SWAT alignments performed. 16 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.038 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.838 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.838 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.838 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 32, in 16 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180116
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  969937
 10  78501
 20  126
 30  6
 40  4
 130  2
min no. words: 0 at 5
max no. words: 129 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.606 Mbytes in 4 blocks
93668 words; after pruning: 93650
Sorting words ... Done

10  78639
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
1.008 Mbytes allocated -- total 7.560 Mbytes
.... Done
Total space allocated: 7.560 Mbytes; currently free: 1.776 Mbytes in 9 blocks
# pass words: 8735, #fail words: 0
Quickalign: 212 successes, 0 failures
4419 SWAT alignments performed. 212 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.434 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.186 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.186 Mbytes in 10 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.186 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1850, in 212 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p45g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180116
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  970049
 10  78401
 20  118
 30  6
 130  2
min no. words: 0 at 5
max no. words: 129 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.609 Mbytes in 4 blocks
93326 words; after pruning: 93208
Sorting words ... Done

10  78527
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
1.008 Mbytes allocated -- total 7.560 Mbytes
.
descrip_buffer expanded. Done
Total space allocated: 7.560 Mbytes; currently free: 1.780 Mbytes in 8 blocks
# pass words: 4445, #fail words: 14331
Quickalign: 275 successes, 123 failures
2368 SWAT alignments performed. 389 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.416 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.168 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.170 Mbytes in 10 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.170 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 19763, in 389 lists, size: 0.020 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p45g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180117
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  975973
 10  72603
min no. words: 0 at 5
max no. words: 6 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.191 Mbytes in 3 blocks
80470 words; after pruning: 79966
Sorting words ... Done

10  72603
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.048 Mbytes; currently free: 0.450 Mbytes in 8 blocks
# pass words: 696, #fail words: 2252
Quickalign: 1 successes, 1 failures
533 SWAT alignments performed. 2 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.044 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.823 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.823 Mbytes in 6 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.823 Mbytes in 6 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 89, in 2 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p45g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180117
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.299 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  976005
 10  72571
min no. words: 0 at 5
max no. words: 6 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.191 Mbytes in 3 blocks
80470 words; after pruning: 79916
Sorting words ... Done

11  77228
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
.. Done
Total space allocated: 6.552 Mbytes; currently free: 0.947 Mbytes in 8 blocks
# pass words: 2387, #fail words: 5569
Quickalign: 42 successes, 39 failures
2427 SWAT alignments performed. 77 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.536 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.315 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.315 Mbytes in 8 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.315 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 4342, in 77 lists, size: 0.004 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p45g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180120
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.340 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.300 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.300 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  976463
 10  72113
min no. words: 0 at 5
max no. words: 6 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.195 Mbytes in 3 blocks
79968 words; after pruning: 79370
Sorting words ... Done

11  76722
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.956 Mbytes in 8 blocks
# pass words: 811, #fail words: 1363
Quickalign: 22 successes, 76 failures
739 SWAT alignments performed. 91 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.531 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.311 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.311 Mbytes in 8 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.311 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 14996, in 91 lists, size: 0.015 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p45g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180120
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  977439
 10  71137
min no. words: 0 at 5
max no. words: 6 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.202 Mbytes in 3 blocks
78818 words; after pruning: 78266
Sorting words ... Done

10  71137
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.048 Mbytes; currently free: 0.474 Mbytes in 8 blocks
# pass words: 634, #fail words: 2206
Quickalign: 16 successes, 10 failures
540 SWAT alignments performed. 20 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.058 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.841 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.841 Mbytes in 9 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.841 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 691, in 20 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180121
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  203462
 10  58680
 20  2
min no. words: 0 at 5
max no. words: 15 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.327 Mbytes in 3 blocks
78818 words; after pruning: 77606
Sorting words ... Done

9  58682
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes

descrip_buffer expanded. Done
Total space allocated: 2.520 Mbytes; currently free: 0.358 Mbytes in 6 blocks
# pass words: 1224, #fail words: 6986
Quickalign: 0 successes, 0 failures
1134 SWAT alignments performed. 0 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.795 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 2.520 Mbytes; currently free: 1.795 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.795 Mbytes in 6 blocks
Total space allocated: 2.520 Mbytes; currently free: 1.795 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180121
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  978015
 10  70561
min no. words: 0 at 5
max no. words: 6 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.205 Mbytes in 3 blocks
78818 words; after pruning: 77550
Sorting words ... Done

10  70561
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded........ Done
Total space allocated: 6.048 Mbytes; currently free: 0.470 Mbytes in 8 blocks
# pass words: 9844, #fail words: 22686
Quickalign: 21 successes, 21 failures
9704 SWAT alignments performed. 30 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.050 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.832 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.832 Mbytes in 8 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.832 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1695, in 30 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180125
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  980471
 10  68105
min no. words: 0 at 5
max no. words: 6 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.220 Mbytes in 3 blocks
78818 words; after pruning: 74640
Sorting words ... Done

10  68105
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
....
descrip_buffer expanded. Done
Total space allocated: 6.552 Mbytes; currently free: 0.980 Mbytes in 10 blocks
# pass words: 5321, #fail words: 12922
Quickalign: 14 successes, 108 failures
5104 SWAT alignments performed. 111 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.531 Mbytes in 10 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.313 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.313 Mbytes in 11 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.313 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 16058, in 111 lists, size: 0.016 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p45g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180129
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  32324
 10  33177
 20  33
 30  2
min no. words: 0 at 6
max no. words: 24 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.661 Mbytes in 4 blocks
78818 words; after pruning: 67288
Sorting words ... Done

8  33212
Finding subject matches ...0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
.. Done
Total space allocated: 2.520 Mbytes; currently free: 0.925 Mbytes in 7 blocks
# pass words: 3002, #fail words: 6044
Quickalign: 11 successes, 37 failures
2435 SWAT alignments performed. 39 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.520 Mbytes in 8 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.815 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.815 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.815 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2481, in 39 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p45g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180131
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  34903
 10  30606
 20  25
 30  2
min no. words: 0 at 6
max no. words: 24 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.205 Mbytes in 3 blocks
78818 words; after pruning: 57686
Sorting words ... Done

8  30633
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.239 Mbytes in 5 blocks
# pass words: 184, #fail words: 251
Quickalign: 0 successes, 0 failures
176 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.790 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 1.512 Mbytes; currently free: 0.790 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.790 Mbytes in 4 blocks
Total space allocated: 1.512 Mbytes; currently free: 0.790 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180131
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  995211
 10  53365
min no. words: 0 at 5
max no. words: 6 at 482466
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.306 Mbytes in 3 blocks
78818 words; after pruning: 57332
Sorting words ... Done

11  56008
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
... Done
Total space allocated: 6.552 Mbytes; currently free: 1.346 Mbytes in 7 blocks
# pass words: 3609, #fail words: 7655
Quickalign: 0 successes, 0 failures
3537 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.827 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.827 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.827 Mbytes in 6 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.827 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p45g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180139
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  215882
 10  46260
 20  2
min no. words: 0 at 5
max no. words: 13 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.427 Mbytes in 3 blocks
78818 words; after pruning: 57568
Sorting words ... Done

9  46262
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
..0.504 Mbytes allocated -- total 3.024 Mbytes
.. Done
Total space allocated: 3.024 Mbytes; currently free: 0.697 Mbytes in 6 blocks
# pass words: 4855, #fail words: 15505
Quickalign: 0 successes, 3 failures
4522 SWAT alignments performed. 3 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.033 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.823 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.823 Mbytes in 9 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.823 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 235, in 3 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180142
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  216594
 10  45548
 20  2
min no. words: 0 at 5
max no. words: 13 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.432 Mbytes in 3 blocks
78818 words; after pruning: 56488
Sorting words ... Done

9  45550
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 1.472 Mbytes in 7 blocks
# pass words: 11931, #fail words: 0
Quickalign: 0 successes, 0 failures
341 SWAT alignments performed. 0 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.803 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 3.528 Mbytes; currently free: 2.803 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.803 Mbytes in 6 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.803 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180142
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  35241
 10  30274
 20  19
 30  2
min no. words: 0 at 6
max no. words: 24 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.210 Mbytes in 3 blocks
78818 words; after pruning: 56610
Sorting words ... Done

8  30295
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
 Done
Total space allocated: 2.520 Mbytes; currently free: 1.249 Mbytes in 7 blocks
# pass words: 34032, #fail words: 0
Quickalign: 0 successes, 0 failures
985 SWAT alignments performed. 0 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.795 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 2.520 Mbytes; currently free: 1.795 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.795 Mbytes in 6 blocks
Total space allocated: 2.520 Mbytes; currently free: 1.795 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180143
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment4.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.302 Mbytes in 2 blocks
Finding words ...
 0  4
 10  150
 20  82
 30  30
 40  68
 50  104
 60  156
 70  116
 80  76
 90  76
 100  56
 110  16
 120  40
 130  22
 140  8
 150  10
 160  4
 170  4
 210  2
min no. words: 0 at 358
max no. words: 206 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 1.008 Mbytes
 Done
Total space allocated: 1.008 Mbytes; currently free: 0.466 Mbytes in 3 blocks
78818 words; after pruning: 56982
Sorting words ... Done

5  1020
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
... Done
Total space allocated: 1.512 Mbytes; currently free: 0.234 Mbytes in 6 blocks
# pass words: 26235, #fail words: 0
Quickalign: 55 successes, 0 failures
3870 SWAT alignments performed. 55 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.523 Mbytes in 5 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.825 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.825 Mbytes in 11 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.825 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 141, in 55 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180143
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  970246
 10  78172
 20  134
 30  22
 190  2
min no. words: 0 at 5
max no. words: 190 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.606 Mbytes in 4 blocks
93668 words; after pruning: 93650
Sorting words ... Done

10  78330
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes
1.008 Mbytes allocated -- total 8.064 Mbytes
1.008 Mbytes allocated -- total 9.072 Mbytes
.... Done
Total space allocated: 9.072 Mbytes; currently free: 3.288 Mbytes in 9 blocks
# pass words: 10418, #fail words: 0
Quickalign: 321 successes, 0 failures
4975 SWAT alignments performed. 321 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 9.072 Mbytes; currently free: 7.945 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 9.072 Mbytes; currently free: 7.696 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 9.072 Mbytes; currently free: 7.697 Mbytes in 9 blocks
Total space allocated: 9.072 Mbytes; currently free: 7.697 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2222, in 321 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p45g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180143
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.327 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.280 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  970359
 10  78061
 20  132
 30  22
 190  2
min no. words: 0 at 5
max no. words: 190 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.608 Mbytes in 4 blocks
93440 words; after pruning: 93362
Sorting words ... Done

10  78217
Finding subject matches ...0.504 Mbytes allocated -- total 6.048 Mbytes
1.008 Mbytes allocated -- total 7.056 Mbytes
1.008 Mbytes allocated -- total 8.064 Mbytes
.
descrip_buffer expanded. Done
Total space allocated: 8.064 Mbytes; currently free: 2.283 Mbytes in 9 blocks
# pass words: 4559, #fail words: 16294
Quickalign: 310 successes, 152 failures
2459 SWAT alignments performed. 439 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 8.064 Mbytes; currently free: 6.915 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 8.064 Mbytes; currently free: 6.666 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 8.064 Mbytes; currently free: 6.668 Mbytes in 10 blocks
Total space allocated: 8.064 Mbytes; currently free: 6.668 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 23811, in 439 lists, size: 0.024 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p45g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180144
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  977929
 10  70645
 70  2
min no. words: 0 at 1
max no. words: 64 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.209 Mbytes in 3 blocks
77708 words; after pruning: 77154
Sorting words ... Done

10  70647
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
0.504 Mbytes allocated -- total 7.056 Mbytes

descrip_buffer expanded Done
Total space allocated: 7.056 Mbytes; currently free: 1.500 Mbytes in 9 blocks
# pass words: 455, #fail words: 5156
Quickalign: 16 successes, 0 failures
397 SWAT alignments performed. 13 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 6.079 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.864 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.864 Mbytes in 10 blocks
Total space allocated: 7.056 Mbytes; currently free: 5.864 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 275, in 13 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p45g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180144
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  977971
 10  70603
 70  2
min no. words: 0 at 1
max no. words: 64 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.209 Mbytes in 3 blocks
77708 words; after pruning: 77100
Sorting words ... Done

11  74618
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.. Done
Total space allocated: 6.048 Mbytes; currently free: 0.488 Mbytes in 8 blocks
# pass words: 2377, #fail words: 6991
Quickalign: 60 successes, 15 failures
2420 SWAT alignments performed. 72 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.065 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.849 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.849 Mbytes in 7 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.849 Mbytes in 7 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2594, in 72 lists, size: 0.003 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p45g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180146
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.343 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.304 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  978329
 10  70245
 70  2
min no. words: 0 at 1
max no. words: 64 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.212 Mbytes in 3 blocks
77330 words; after pruning: 76700
Sorting words ... Done

11  74236
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
 Done
Total space allocated: 6.552 Mbytes; currently free: 0.997 Mbytes in 8 blocks
# pass words: 668, #fail words: 2139
Quickalign: 17 successes, 96 failures
738 SWAT alignments performed. 113 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.559 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.344 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.344 Mbytes in 9 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.344 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 14068, in 113 lists, size: 0.014 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p45g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180147
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  979695
 10  68879
 70  2
min no. words: 0 at 1
max no. words: 64 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.222 Mbytes in 3 blocks
75722 words; after pruning: 75108
Sorting words ... Done

10  68881
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.552 Mbytes; currently free: 1.024 Mbytes in 10 blocks
# pass words: 450, #fail words: 5146
Quickalign: 19 successes, 2 failures
402 SWAT alignments performed. 21 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.593 Mbytes in 10 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.381 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.381 Mbytes in 11 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.381 Mbytes in 11 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 516, in 21 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180147
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  204352
 10  57784
 20  6
 50  2
min no. words: 0 at 6
max no. words: 45 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.345 Mbytes in 3 blocks
75722 words; after pruning: 74810
Sorting words ... Done

9  57792
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes

descrip_buffer expanded. Done
Total space allocated: 3.024 Mbytes; currently free: 0.640 Mbytes in 8 blocks
# pass words: 1150, #fail words: 6753
Quickalign: 58 successes, 0 failures
1224 SWAT alignments performed. 40 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.062 Mbytes in 9 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.354 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.354 Mbytes in 10 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.354 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 755, in 40 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180148
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  980298
 10  68276
 40  2
min no. words: 0 at 1
max no. words: 38 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.226 Mbytes in 3 blocks
75722 words; after pruning: 74358
Sorting words ... Done

10  68278
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded........ Done
Total space allocated: 6.048 Mbytes; currently free: 0.520 Mbytes in 8 blocks
# pass words: 9289, #fail words: 23054
Quickalign: 41 successes, 14 failures
9192 SWAT alignments performed. 52 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.083 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.872 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.872 Mbytes in 8 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.872 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1811, in 52 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180152
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  984089
 10  64485
 40  2
min no. words: 0 at 1
max no. words: 38 at 0
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.248 Mbytes in 3 blocks
75722 words; after pruning: 69958
Sorting words ... Done

10  64487
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
0.504 Mbytes allocated -- total 6.552 Mbytes
....
descrip_buffer expanded Done
Total space allocated: 6.552 Mbytes; currently free: 1.038 Mbytes in 9 blocks
# pass words: 4977, #fail words: 12869
Quickalign: 20 successes, 109 failures
4970 SWAT alignments performed. 125 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.565 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.353 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.354 Mbytes in 10 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.354 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 15316, in 125 lists, size: 0.015 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p45g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180155
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  33786
 10  31734
 20  12
 30  2
 60  2
min no. words: 0 at 6
max no. words: 53 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.206 Mbytes in 3 blocks
75722 words; after pruning: 58272
Sorting words ... Done

8  31750
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
.. Done
Total space allocated: 2.520 Mbytes; currently free: 0.998 Mbytes in 8 blocks
# pass words: 2701, #fail words: 4874
Quickalign: 13 successes, 31 failures
2207 SWAT alignments performed. 39 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.549 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.345 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.345 Mbytes in 9 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.345 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 2158, in 39 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p45g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180157
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  36132
 10  29391
 20  10
 30  1
 50  2
min no. words: 0 at 6
max no. words: 50 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.244 Mbytes in 3 blocks
75722 words; after pruning: 50816
Sorting words ... Done

8  29404
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.294 Mbytes in 5 blocks
# pass words: 168, #fail words: 277
Quickalign: 0 successes, 0 failures
158 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.810 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 1.512 Mbytes; currently free: 0.810 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.810 Mbytes in 4 blocks
Total space allocated: 1.512 Mbytes; currently free: 0.810 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p45g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180157
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  1001079
 10  47495
 40  2
min no. words: 0 at 1
max no. words: 36 at 1048575
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.345 Mbytes in 3 blocks
75722 words; after pruning: 50476
Sorting words ... Done

11  49308
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
... Done
Total space allocated: 6.048 Mbytes; currently free: 0.899 Mbytes in 6 blocks
# pass words: 3101, #fail words: 6885
Quickalign: 0 successes, 0 failures
3039 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.346 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 5.346 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.346 Mbytes in 5 blocks
Total space allocated: 6.048 Mbytes; currently free: 5.346 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p45g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180204
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  219882
 10  42258
 20  2
 50  2
min no. words: 0 at 1
max no. words: 41 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.466 Mbytes in 3 blocks
75722 words; after pruning: 50702
Sorting words ... Done

9  42262
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
... Done
Total space allocated: 3.024 Mbytes; currently free: 0.752 Mbytes in 7 blocks
# pass words: 4269, #fail words: 12784
Quickalign: 0 successes, 3 failures
3990 SWAT alignments performed. 3 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.054 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.347 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.347 Mbytes in 8 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.347 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 294, in 3 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180207
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  220448
 10  41692
 20  2
 50  2
min no. words: 0 at 1
max no. words: 41 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.470 Mbytes in 3 blocks
75722 words; after pruning: 49890
Sorting words ... Done

9  41696
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
 Done
Total space allocated: 3.024 Mbytes; currently free: 0.766 Mbytes in 7 blocks
# pass words: 9814, #fail words: 0
Quickalign: 5 successes, 1 failures
260 SWAT alignments performed. 6 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.064 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.356 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.356 Mbytes in 8 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.356 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 125, in 6 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180207
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.344 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.306 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  36435
 10  29095
 20  4
 30  2
min no. words: 0 at 6
max no. words: 25 at 0
avg no. words: 0.0 Done
Total space allocated: 1.008 Mbytes; currently free: 0.250 Mbytes in 3 blocks
75722 words; after pruning: 49644
Sorting words ... Done

8  29101
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
0.504 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.545 Mbytes in 7 blocks
# pass words: 27886, #fail words: 0
Quickalign: 1 successes, 0 failures
814 SWAT alignments performed. 1 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.056 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
 Done
Total space allocated: 3.528 Mbytes; currently free: 2.356 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 3.528 Mbytes; currently free: 2.356 Mbytes in 9 blocks
Total space allocated: 3.528 Mbytes; currently free: 2.356 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 22, in 1 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180207
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.345 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.345 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment5.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.307 Mbytes in 2 blocks
Finding words ...
 10  104
 20  106
 30  88
 40  118
 50  146
 60  134
 70  102
 80  72
 90  68
 100  46
 110  18
 120  8
 130  12
 170  2
min no. words: 1 at 792
max no. words: 169 at 0
avg no. words: 0.0 Done
Total space allocated: 0.504 Mbytes; currently free: 0.002 Mbytes in 2 blocks
75722 words; after pruning: 49834
Sorting words ... Done

5  1024
Finding subject matches ...0.504 Mbytes allocated -- total 1.008 Mbytes
0.504 Mbytes allocated -- total 1.512 Mbytes
... Done
Total space allocated: 1.512 Mbytes; currently free: 0.298 Mbytes in 6 blocks
# pass words: 21622, #fail words: 0
Quickalign: 31 successes, 0 failures
3320 SWAT alignments performed. 31 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.551 Mbytes in 5 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.859 Mbytes in 11 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.859 Mbytes in 10 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.859 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 133, in 31 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 10 -minscore 180 -masklevel 1 -bandwidth 1 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180207
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.329 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.329 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.283 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.283 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  971364
 10  77074
 20  110
 30  16
 40  8
 50  1
 70  1
 140  2
min no. words: 0 at 5
max no. words: 134 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.619 Mbytes in 4 blocks
91660 words; after pruning: 91642
Sorting words ... Done

10  77212
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
.... Done
Total space allocated: 6.552 Mbytes; currently free: 0.796 Mbytes in 6 blocks
# pass words: 13225, #fail words: 0
Quickalign: 44 successes, 19 failures
4626 SWAT alignments performed. 63 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.446 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 6.552 Mbytes; currently free: 5.203 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 6.552 Mbytes; currently free: 5.203 Mbytes in 6 blocks
Total space allocated: 6.552 Mbytes; currently free: 5.203 Mbytes in 6 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 957, in 63 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p51g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180207
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.329 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.329 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.284 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.284 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  971665
 10  76781
 20  111
 30  8
 40  9
 140  2
min no. words: 0 at 5
max no. words: 132 at 0
avg no. words: 0.00.504 Mbytes allocated -- total 5.544 Mbytes
 Done
Total space allocated: 5.544 Mbytes; currently free: 0.626 Mbytes in 4 blocks
90774 words; after pruning: 90636
Sorting words ... Done

10  76911
Finding subject matches ...1.008 Mbytes allocated -- total 6.552 Mbytes
1.008 Mbytes allocated -- total 7.560 Mbytes
.
descrip_buffer expanded Done
Total space allocated: 7.560 Mbytes; currently free: 1.816 Mbytes in 8 blocks
# pass words: 3524, #fail words: 12405
Quickalign: 232 successes, 71 failures
1879 SWAT alignments performed. 299 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.446 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 7.560 Mbytes; currently free: 6.204 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 7.560 Mbytes; currently free: 6.205 Mbytes in 9 blocks
Total space allocated: 7.560 Mbytes; currently free: 6.205 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 13931, in 299 lists, size: 0.014 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p51g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 1200 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180208
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.339 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.339 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.298 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.298 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  976035
 10  72501
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.185 Mbytes in 3 blocks
81268 words; after pruning: 80866
Sorting words ... Done

10  72541
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.048 Mbytes; currently free: 0.439 Mbytes in 8 blocks
# pass words: 597, #fail words: 3456
Quickalign: 2 successes, 0 failures
496 SWAT alignments performed. 2 pairs have score >= 1200
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.037 Mbytes in 7 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.815 Mbytes in 8 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.815 Mbytes in 7 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.815 Mbytes in 7 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 114, in 2 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/cut1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p51g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 1 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180208
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.339 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.339 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.298 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.298 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  976067
 10  72469
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.185 Mbytes in 3 blocks
81268 words; after pruning: 80826
Sorting words ... Done

11  77406
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.. Done
Total space allocated: 6.048 Mbytes; currently free: 0.432 Mbytes in 7 blocks
# pass words: 2865, #fail words: 5762
Quickalign: 47 successes, 35 failures
2868 SWAT alignments performed. 80 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.024 Mbytes in 6 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.801 Mbytes in 7 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.802 Mbytes in 6 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.802 Mbytes in 6 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 5081, in 80 lists, size: 0.005 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/cut2.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p51g.matrix -gap_init -33 -ins_gap_ext -5 -del_gap_ext -4 -minmatch 11 -minscore 300 -masklevel 90 -bandwidth 40 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180211
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  977907
 10  70629
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.199 Mbytes in 3 blocks
79184 words; after pruning: 78676
Sorting words ... Done

11  75370
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
 Done
Total space allocated: 6.048 Mbytes; currently free: 0.732 Mbytes in 6 blocks
# pass words: 413, #fail words: 1275
Quickalign: 0 successes, 0 failures
409 SWAT alignments performed. 0 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.320 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 5.320 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.320 Mbytes in 5 blocks
Total space allocated: 6.048 Mbytes; currently free: 5.320 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/14p51g.matrix -gap_init -35 -ins_gap_ext -7 -del_gap_ext -6 -minmatch 10 -minscore 800 -masklevel 1 -bandwidth 20 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180212
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  977870
 10  70666
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.199 Mbytes in 3 blocks
79184 words; after pruning: 78722
Sorting words ... Done

10  70706
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes

descrip_buffer expanded Done
Total space allocated: 6.048 Mbytes; currently free: 0.468 Mbytes in 9 blocks
# pass words: 583, #fail words: 3446
Quickalign: 6 successes, 7 failures
504 SWAT alignments performed. 11 pairs have score >= 800
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.055 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.837 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.837 Mbytes in 10 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.837 Mbytes in 10 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 769, in 11 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/alu.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/18p51g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 400 -masklevel 10 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180212
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  203962
 10  58140
 20  18
 30  10
 40  12
 50  2
min no. words: 0 at 4
max no. words: 44 at 62668
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.323 Mbytes in 3 blocks
79184 words; after pruning: 78264
Sorting words ... Done

9  58182
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes

descrip_buffer expanded. Done
Total space allocated: 4.032 Mbytes; currently free: 1.597 Mbytes in 10 blocks
# pass words: 1585, #fail words: 5800
Quickalign: 13 successes, 2 failures
1555 SWAT alignments performed. 14 pairs have score >= 400
Making reversed pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 3.036 Mbytes in 11 blocks
Printing matches ...  Done
Total space allocated: 4.032 Mbytes; currently free: 2.818 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.818 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.818 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 399, in 14 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/humsines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p51g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180212
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  978456
 10  70080
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.203 Mbytes in 3 blocks
79184 words; after pruning: 77946
Sorting words ... Done

10  70120
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.
descrip_buffer expanded
descrip_buffer expanded......... Done
Total space allocated: 6.048 Mbytes; currently free: 0.465 Mbytes in 9 blocks
# pass words: 10904, #fail words: 20882
Quickalign: 26 successes, 7 failures
10733 SWAT alignments performed. 16 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.048 Mbytes in 8 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 4.830 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 4.830 Mbytes in 9 blocks
Total space allocated: 6.048 Mbytes; currently free: 4.830 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 560, in 16 lists, size: 0.001 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/humlines.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p51g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 10 -minscore 225 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180217
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  980902
 10  67634
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.217 Mbytes in 3 blocks
79184 words; after pruning: 75058
Sorting words ... Done

10  67674
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
....
descrip_buffer expanded. Done
Total space allocated: 6.048 Mbytes; currently free: 0.623 Mbytes in 9 blocks
# pass words: 5551, #fail words: 11986
Quickalign: 3 successes, 4 failures
5387 SWAT alignments performed. 0 pairs have score >= 225
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.193 Mbytes in 9 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 5.193 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.193 Mbytes in 9 blocks
Total space allocated: 6.048 Mbytes; currently free: 5.193 Mbytes in 9 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/mirs.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p51g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 180 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180221
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  30637
 10  34783
 20  94
 30  6
 40  11
 50  4
 80  1
min no. words: 0 at 4
max no. words: 80 at 13107
avg no. words: 0.00.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.621 Mbytes in 4 blocks
79184 words; after pruning: 75170
Sorting words ... Done

8  34899
Finding subject matches ...0.504 Mbytes allocated -- total 2.016 Mbytes
0.504 Mbytes allocated -- total 2.520 Mbytes
.. Done
Total space allocated: 2.520 Mbytes; currently free: 0.882 Mbytes in 7 blocks
# pass words: 3804, #fail words: 6814
Quickalign: 18 successes, 21 failures
2984 SWAT alignments performed. 30 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.518 Mbytes in 8 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.812 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.812 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.812 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 1506, in 30 lists, size: 0.002 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/mir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p51g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 8 -minscore 250 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180223
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  32436
 10  33000
 20  78
 30  6
 40  11
 50  4
 80  1
min no. words: 0 at 4
max no. words: 80 at 13107
avg no. words: 0.00.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.656 Mbytes in 4 blocks
79184 words; after pruning: 68110
Sorting words ... Done

8  33100
Finding subject matches ...0.504 Mbytes allocated -- total 2.016 Mbytes
 Done
Total space allocated: 2.016 Mbytes; currently free: 0.687 Mbytes in 5 blocks
# pass words: 273, #fail words: 316
Quickalign: 0 successes, 0 failures
268 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.290 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 2.016 Mbytes; currently free: 1.290 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.290 Mbytes in 5 blocks
Total space allocated: 2.016 Mbytes; currently free: 1.290 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/retrovir.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/20p51g.matrix -gap_init -30 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 11 -minscore 250 -masklevel 90 -bandwidth 14 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180223
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
4.536 Mbytes allocated -- total 5.040 Mbytes
Finding words ...
 0  987133
 10  61403
 20  21
 30  10
 40  9
min no. words: 0 at 1
max no. words: 37 at 209795
avg no. words: 0.0 Done
Total space allocated: 5.040 Mbytes; currently free: 0.253 Mbytes in 3 blocks
79184 words; after pruning: 67818
Sorting words ... Done

11  65036
Finding subject matches ...0.504 Mbytes allocated -- total 5.544 Mbytes
0.504 Mbytes allocated -- total 6.048 Mbytes
.... Done
Total space allocated: 6.048 Mbytes; currently free: 0.786 Mbytes in 6 blocks
# pass words: 4419, #fail words: 8171
Quickalign: 0 successes, 0 failures
4329 SWAT alignments performed. 0 pairs have score >= 250
Making reversed pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.320 Mbytes in 5 blocks
Printing matches ...  Done
Total space allocated: 6.048 Mbytes; currently free: 5.320 Mbytes in 6 blocks
Checking pairs ... Done
Total space allocated: 6.048 Mbytes; currently free: 5.320 Mbytes in 5 blocks
Total space allocated: 6.048 Mbytes; currently free: 5.320 Mbytes in 5 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/l1.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/25p49g.matrix -gap_init -27 -ins_gap_ext -6 -del_gap_ext -5 -minmatch 9 -minscore 300 -masklevel 90 -bandwidth 14 -raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180233
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  210174
 10  51928
 20  18
 30  10
 40  12
 50  2
min no. words: 0 at 4
max no. words: 44 at 62668
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.374 Mbytes in 3 blocks
79184 words; after pruning: 68010
Sorting words ... Done

9  51970
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
.0.504 Mbytes allocated -- total 3.024 Mbytes
.... Done
Total space allocated: 3.024 Mbytes; currently free: 0.636 Mbytes in 7 blocks
# pass words: 6056, #fail words: 15344
Quickalign: 0 successes, 6 failures
5617 SWAT alignments performed. 6 pairs have score >= 300
Making reversed pairs ... Done
Total space allocated: 3.024 Mbytes; currently free: 2.024 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.814 Mbytes in 9 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.814 Mbytes in 8 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.814 Mbytes in 8 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 219, in 6 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple1.matrix -gap_init -40 -ins_gap_ext -15 -del_gap_ext -15 -minmatch 9 -minscore 180 -masklevel 25 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180237
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
1.512 Mbytes allocated -- total 2.016 Mbytes
Finding words ...
 0  210188
 10  51930
 20  12
 30  10
 40  4
min no. words: 0 at 4
max no. words: 32 at 0
avg no. words: 0.0 Done
Total space allocated: 2.016 Mbytes; currently free: 0.376 Mbytes in 3 blocks
79184 words; after pruning: 67626
Sorting words ... Done

9  51956
Finding subject matches ...0.504 Mbytes allocated -- total 2.520 Mbytes
 Done
Total space allocated: 2.520 Mbytes; currently free: 0.142 Mbytes in 6 blocks
# pass words: 15252, #fail words: 0
Quickalign: 7 successes, 0 failures
359 SWAT alignments performed. 7 pairs have score >= 180
Making reversed pairs ... Done
Total space allocated: 2.520 Mbytes; currently free: 1.528 Mbytes in 6 blocks
Printing matches ... 0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.822 Mbytes in 10 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.822 Mbytes in 9 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.822 Mbytes in 9 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 174, in 7 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/simple.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/simple.matrix -gap_init -35 -ins_gap_ext -10 -del_gap_ext -10 -minmatch 8 -minscore 200 -masklevel 75 -bandwidth 4 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180237
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
0.504 Mbytes allocated -- total 1.008 Mbytes
Finding words ...
 0  32509
 10  32963
 20  64
min no. words: 0 at 4
max no. words: 18 at 21781
avg no. words: 0.00.504 Mbytes allocated -- total 1.512 Mbytes
 Done
Total space allocated: 1.512 Mbytes; currently free: 0.662 Mbytes in 4 blocks
79184 words; after pruning: 66878
Sorting words ... Done

8  33027
Finding subject matches ...0.504 Mbytes allocated -- total 2.016 Mbytes
. Done
Total space allocated: 2.016 Mbytes; currently free: 0.428 Mbytes in 6 blocks
# pass words: 41496, #fail words: 0
Quickalign: 5 successes, 0 failures
1200 SWAT alignments performed. 5 pairs have score >= 200
Making reversed pairs ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.024 Mbytes in 7 blocks
Printing matches ... 0.504 Mbytes allocated -- total 2.520 Mbytes
0.504 Mbytes allocated -- total 3.024 Mbytes
0.504 Mbytes allocated -- total 3.528 Mbytes
0.504 Mbytes allocated -- total 4.032 Mbytes
 Done
Total space allocated: 4.032 Mbytes; currently free: 2.822 Mbytes in 12 blocks
Checking pairs ... Done
Total space allocated: 4.032 Mbytes; currently free: 2.822 Mbytes in 12 blocks
Total space allocated: 4.032 Mbytes; currently free: 2.822 Mbytes in 12 blocks
Total # pairs: 1000, size: 0.044 Mbytes
Total # segment blocks: 1, size: 0.060 Mbytes
Total # diffs: 62, in 5 lists, size: 0.000 Mbytes


/home/seqanal/phrap/cross_match /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked /home/seqanal//RepeatMasker20020713/Libraries/at.lib -matrix /home/seqanal//RepeatMasker20020713/Matrices/at.matrix -gap_init -10 -ins_gap_ext -3 -del_gap_ext -3 -minmatch 5 -minscore 21 -masklevel 95 -bandwidth 2 -raw -word_raw 
cross_match version 0.990329
Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
Run date:time  060309:180238
 Done
Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks
Reading query file into memory ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.341 Mbytes in 2 blocks
Allocating align_entries ... Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Reading quality files ...

NO QUALITY FILE /root/RM_25781.ThuMar9180000CET2006/repeat.seq.fragment6.masked.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 0.504 Mbytes; currently free: 0.301 Mbytes in 2 blocks
Finding words ...
 10  72
 20  94
 30  80
 40  124
 50  88
 60  80
 70  84
 80  76
 90  60
 100  56
 110  46
 120  28
 130  34
 140  20
 150  22
 160  10
 170  18
 180  12
 190  8
 200  4
 210  4
 220  4
min no. words: 3 at 102
max no. words: 215 at 373
avg no. words: 0.00.504 Mbytes allocated -- total 1.008 Mbytes
 Done
Total space allocated: 1.008 Mbytes; currently free: 0.415 Mbytes in 3 blocks
79184 words; after pruning: 66984
Sorting words ... Done

5  1024
Finding subject matches ...0.504 Mbytes allocated -- total 1.512 Mbytes
.... Done
Total space allocated: 1.512 Mbytes; currently free: 0.445 Mbytes in 4 blocks
# pass words: 24648, #fail words: 0
Quickalign: 0 successes, 0 failures
4431 SWAT alignments performed. 0 pairs have score >= 21
Making reversed pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.784 Mbytes in 4 blocks
Printing matches ...  Done
Total space allocated: 1.512 Mbytes; currently free: 0.784 Mbytes in 5 blocks
Checking pairs ... Done
Total space allocated: 1.512 Mbytes; currently free: 0.784 Mbytes in 4 blocks
Total space allocated: 1.512 Mbytes; currently free: 0.784 Mbytes in 4 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes