Command line: [exonerate -m p2g --showtargetgff -q selm1.fa.U_to_X -t gi|511782574|gb|CM001960.1|.fastasubseq]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000077_2.0 # Protein # Selenoprotein M (SelM) # Human (Homo sapiens) 
        Target: gi|511782574|gb|CM001960.1|:subseq(13946501,100312) Chlorocebus sabaeus isolate 1994-021 chromosome 19, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 702
   Query range: 0 -> 145
  Target range: 52493 -> 49999

     1 : MetSerLeuLeuLeuProProLeuAlaLeuLeuLeuLeuLeuAlaAlaLeuValAlaPro :    20
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         MetSerLeuLeuLeuProProLeuAlaLeuLeuLeuLeuLeuAlaAlaLeuValAlaPro
 52493 : ATGAGCCTCCTGTTGCCTCCGCTGGCGCTGCTGCTGCTTCTCGCGGCGCTTGTGGCCCCA : 52436

    21 : AlaThrAlaAlaThrAlaTyrArgProAspTrpAsnArgLeuSerGlyLeuThrArgAla :    40
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         AlaThrAlaAlaThrAlaTyrArgProAspTrpAsnArgLeuSerGlyLeuThrArgAla
 52435 : GCCACAGCCGCCACTGCCTACCGGCCGGACTGGAATCGTCTGAGCGGCCTGACCCGCGCC : 52376

    41 : ArgValGlu  >>>> Target Intron 1 >>>>  ThrCysGlyGlyUnkGlnLeuA :    51
         |||||||||           1422 bp           ||||||||||||   |||||||
         ArgValGlu++                         ++ThrCysGlyGly***GlnLeuA
 52375 : CGGGTAGAGgt.........................agACCTGTGGGGGATGACAGCTGA : 50921

    52 : snArgLeuLysGlu  >>>> Target Intron 2 >>>>  ValLysAlaPheValTh :    61
         ||||||||||||||            216 bp           |||||||||||||||||
         snArgLeuLysGlu++                         ++ValLysAlaPheValTh
 50920 : ATCGCCTAAAGGAGgt.........................agGTGAAGGCTTTCGTCAC : 50675

    62 : rGlnAspIleProPhe{Ty}  >>>> Target Intron 3 >>>>  {r}HisAsnLe :    70
         ||||||||||||||||{||}            342 bp           {|}||||||||
         rGlnAspIleProPhe{Ty}++                         ++{r}HisAsnLe
 50674 : CCAGGACATTCCATTC{TA}gt.........................ag{T}CACAACCT : 50306

    71 : uValMetLysHisLeuProGlyAlaAspProGluLeuValLeuLeuGlyArgArgTyrGl :    90
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         uValMetLysHisLeuProGlyAlaAspProGluLeuValLeuLeuGlyArgArgTyrGl
 50305 : GGTGATGAAACACCTCCCTGGGGCCGACCCTGAGCTCGTGCTGCTGGGCCGCCGCTACGA : 50246

    91 : uGluLeuGlu  >>>> Target Intron 4 >>>>  ArgIleProLeuSerGluMet :   100
         ||||||||||            79 bp            |||||||||||||||||||||
         uGluLeuGlu++                         ++ArgIleProLeuSerGluMet
 50245 : GGAACTGGAGgt.........................agCGCATACCGCTCAGTGAAATG : 50137

   101 : ThrArgGluGluIleAsnAlaLeuValGlnGluLeuGlyPheTyrArgLysAlaAlaPro :   120
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         ThrArgGluGluIleAsnAlaLeuValGlnGluLeuGlyPheTyrArgLysAlaAlaPro
 50136 : ACCCGCGAAGAGATCAACGCGCTGGTGCAGGAGCTCGGTTTCTACCGCAAGGCGGCGCCC : 50077

   121 : AspAlaGlnValProProGluTyrValTrpAlaProAlaLysProProGluGluThrSer :   140
         |||||||||||||||||||||||||||||||||||||||!:!||||||||||||||||||
         AspAlaGlnValProProGluTyrValTrpAlaProAlaArgProProGluGluThrSer
 50076 : GACGCGCAGGTGCCCCCCGAGTACGTGTGGGCGCCCGCTAGGCCCCCGGAGGAAACTTCG : 50017

   141 : AspHisAlaAspLeu :   145
         |||||||||||||||
         AspHisAlaAspLeu
 50016 : GACCACGCCGACCTG : 50000

vulgar: SPP00000077_2.0 0 145 . gi|511782574|gb|CM001960.1|:subseq(13946501,100312) 52493 49999 - 702 M 43 129 5 0 2 I 0 1418 3 0 2 M 12 36 5 0 2 I 0 212 3 0 2 M 11 33 S 0 2 5 0 2 I 0 338 3 0 2 S 1 1 M 26 78 5 0 2 I 0 75 3 0 2 M 52 156
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	gene	50000	52493	702	-	.	gene_id 1 ; sequence SPP00000077_2.0 ; gene_orientation +
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	cds	52365	52493	.	-	.	
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	exon	52365	52493	.	-	.	insertions 0 ; deletions 0
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	splice5	52363	52364	.	-	.	intron_id 1 ; splice_site "GT"
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	intron	50943	52364	.	-	.	intron_id 1
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	splice3	50943	50944	.	-	.	intron_id 0 ; splice_site "AG"
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	cds	50907	50942	.	-	.	
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	exon	50907	50942	.	-	.	insertions 0 ; deletions 0
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	splice5	50905	50906	.	-	.	intron_id 2 ; splice_site "GT"
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	intron	50691	50906	.	-	.	intron_id 2
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	splice3	50691	50692	.	-	.	intron_id 1 ; splice_site "AG"
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	cds	50656	50690	.	-	.	
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	exon	50656	50690	.	-	.	insertions 0 ; deletions 0
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	splice5	50654	50655	.	-	.	intron_id 3 ; splice_site "GT"
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	intron	50314	50655	.	-	.	intron_id 3
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	splice3	50314	50315	.	-	.	intron_id 2 ; splice_site "AG"
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	cds	50235	50313	.	-	.	
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	exon	50235	50313	.	-	.	insertions 0 ; deletions 0
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	splice5	50233	50234	.	-	.	intron_id 4 ; splice_site "GT"
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	intron	50156	50234	.	-	.	intron_id 4
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	splice3	50156	50157	.	-	.	intron_id 3 ; splice_site "AG"
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	cds	50000	50155	.	-	.	
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	exon	50000	50155	.	-	.	insertions 0 ; deletions 0
gi|511782574|gb|CM001960.1|:subseq(13946501,100312)	exonerate:protein2genome:local	similarity	50000	52493	702	-	.	alignment_id 1 ; Query SPP00000077_2.0 ; Align 52494 1 129 ; Align 50943 44 36 ; Align 50691 56 33 ; Align 50313 68 78 ; Align 50156 94 156
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis