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_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
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Blastx evalue: 1e-20
Query name: gi|5107031|gb|AAD39929.1|AF133519_1 thioredoxin reductase 3, partial [Homo sapiens]
Query range: 15-577 (total 577)
Target: /data/www-rg/seblastian_results/17354455/tempfiles/temptarget.fasta
Chromosome: LDJU01000159.1:subseq_1372935,31452_ Strand: -
Positions:
-Exon 1 30699 30762
-Exon 2 29571 29680
-Exon 3 28217 28321
-Exon 4 27908 27980
-Exon 5 26332 26451
-Exon 6 22189 22331
-Exon 7 20674 20789
-Exon 8 19467 19692
-Exon 9 18214 18306
-Exon 10 15581 15657
-Exon 11 14849 15005
-Exon 12 10894 11001
-Exon 13 7243 7338
-Exon 14 5003 5137
-Exon 15 4732 4797
Redox box: no
Query RVKELFSSLGVECNVLELDQVD <---Intron---> DGARVQEVLSEITNQKTVPNIFVNKVHVGGCDQTFQ <---Intron---> AYQSGLLQKL
/||||||||||| |/||||/|| < 1018bp > ||| |||||||||||/|||/|||||||/|| ||||| < 1249bp > |/||||||||
Target QVKELFSSLGVEYNILELDKVD DGASVQEVLSEITNQRTVPSIFVNKVHMGGYDQTFQ AHQSGLLQKL
cgagcttttgggtaatgcgagg gggagcggctgaaacaagcaatgaagcaggtgcatc gccagttcac
ataattcctgtaaattataat aagcgtaattcatcaagctcgtttaatatggaaacta caaggttaat
gtaattttgatgttcgattag ttgcttaaggagcttgatgctttgtaatgtatcatcg atgttgaggt
Query LQEDLAYDYDLIIIGGGSGGLSCAK <---Intron---> EAAILGKKVMVLDFVVPSPQGTSWG <---Intron---> LGGTCVNVGCIPKKLMHQ
|| | |||||||/||||||||/||/ < 236bp > ||||||||||||||||||||||||| < 1456bp > ||||||||||/|||||||
Target LQRDAAYDYDLIVIGGGSGGLACAQ EAAILGKKVMVLDFVVPSPQGTSWG LGGTCVNVGCVPKKLMHQ
ccagggtgtgcagagggtggcgtgc gggatgaagagcgtggctccgattg cggatgaggtgcaacacc
tagaccaaaattttgggcggtcgca accttgaattttatttcccagccg gtggcgtatggtcaattaa
tgatgatttccacctttttttattg atctgagaaggattgcgatgtacg ttctttatattttgaggta
Query AALLGQALCDSRKFGWEYNQQV <---Intron---> RHNWETMTKAIQNHISSLNWGYRLSLREKAVAYVNSYGEFVEHHKIK <---Intron--->
|||||||| ||||||||||||| < 4000bp > /|||||| /|||||| |||| | /||||||||||||||||||||||| < 1399bp >
Target AALLGQALSDSRKFGWEYNQQV KHNWETMAEAIQNHIGSLNWSYGMSLREKAVAYVNSYGEFVEHHKIK
ggctgcgtagtaatgtgtaccg acatgaagggacacagtcatatgattagagggtgattggtggccaaa
ccttgactgacgatggaaaaa taaagactcactaaatgctaggagtctgaactcatacagattaaaata
tctgggaatcagatcggttaa ggccggcgaattacctctatgctggtggggtgctatctaattactaag
Query ATNKKGQETYYTAAQFVIATGERPRYLGIQGDKEYCITS <---Intron---> DDLFSLPYCPGKPLVVGASYVALECAGFLAGFGLDVTVMVRSIL
|||/||||||||| /|||||||||||||||||||/|||| < 981bp > |||||||||||| |||||||||||||||||| ||||||||||||
Target ATNRKGQETYYTAEKFVIATGERPRYLGIQGDKEHCITS DDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSIL
gaaaagcgattaggatgagaggaccttgacggagctaaa ggcttccttcgaatggggttggcgtggtcggagtggagagctac
ccagagaacaaccaatttccgagcgatgtagaaaagtcg aattctcagcgactttgccatctagcgttcgtgtatctttgctt
actaaaggtttttaatcaaatagagtaacactaacttt ttctttgtcctcaaaacgactgtgataatttttcatcatgggact
Query LRGFDQEMAEKVGSYMEQHGVKFLRKFIPVM <---Intron---> VQQLEKGSPGKLKVLAKSTEGTETIEGVYNT <---Intron---> VLLAIG
||||||||||||||||||||||||||||||| < 1160bp > /|||||| ||||||/|||||| ||||||||| < 2556bp > ||||||
Target LRGFDQEMAEKVGSYMEQHGVKFLRKFIPVM IQQLEKGLPGKLKVVAKSTEGPETIEGVYNT VLLAIG
ccgtgcgaggaggttagccggattaatacga acctgagtcgacagggataggcgaagggtaa gttgag
tggtaaatcaatgcataaagtattgattctt taataagtcgatattcaccagcactagtaac tttctg
ttcttaagagagtctgaatttgcaaatatgg tagggatataggaagtacgaaaattaagtca tgaatt
Query RDSCTRKIGLEKIGVKINEK <---Intron---> SGKIPVNDVEQTNVPYVYAVGDILEDKPELTPVAIQSGKLLAQRLFGASLEK <---Intron-
||| |||||||||||||||| < 575bp > /|||||||/|||||||||||||/|| | ||||||||/|||||/|||| ||| < 3847bp
Target RDSSTRKIGLEKIGVKINEK TGKIPVNDMEQTNVPYVYAVGDVLEGKLELTPVAIQAGKLLARRLFGGRLEK
cgttaaaagtgaaggaaaga agaacgagagcaagctgtgggggcggacgcacggacggactgcactggctga
gacccgatgtaatgtataaa cgatctaataacatcatactgattagatatcctctacgattcggttgggtaa
ttctagaacgggttcactg gtcgaaatcgagctgcttcttgttgatatgcttccagacgggtaattgttaag
Query --> CDYINVPTTVFTPLEYGCCGLSEEKAIEVYKKENLE <---Intron---> IYHTLFWPLEWTVAGRENNTCYAKIICNKFDH <---Intron-
> |||/||||||||||||||||||||||||/||||||| < 3555bp > /|||||||||||||||/|||||||||||| |/ < 2105bp
Target CDYVNVPTTVFTPLEYGCCGLSEEKAIEIYKKENLE VYHTLFWPLEWTVAGRDNNTCYAKIICNKLDN
tgtgagcaagtaccgtgttgttggagagataagatg gtcatttccgtagggagaaattgaaataatga
gaatatcccttcctaaggggtcaaactataaaaata taacttgctagctcggaaacgacattgaataa
ttttttatagttcgatcctaatagattaataagtaa atttgcgttggaaccaccttttagatctagct
Query --> DRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDDTIGIHPTCGE <---Intron---> VFTTLEITKSSGLDITQKGCUG
> /||||||||||||||||||||||||||||||||| |||||||||| < 205bp > |||||||||||||| /||||||
Target NRVIGFHILGPNAGEVTQGFAAAMKCGLTKQLLDGTIGIHPTCGE VFTTLEITKSSGLDFSQKGCUG
acgagtcacgcaggggacgtgggaatgcaacccggaagaccatgg gtaatgaaattgcgttcagttg
agttgtattgcacgatcagtccctaggtcaattagctgtaccgga ttcctatcaccgtatcaagggg
cggaatcttggtctgttaatatagatgcgggattcctatctattg acctgaaagagatcccgaccac
*
Sequence until next stop:
TAG
*
Distance CDS-SECIS: 179 ; UGA-SECIS: 182
------- SECIS element -- id:1 -- grade:A ----
Chromosome = LDJU01000159.1:subseq_1372935,31452_ Strand = - Positions = 4552 - 4473
Found by: Infernal (score=33.84) Covels (score=27.35)
Stem2 length = 11 Apical loop length = 16 Insertion in stem2 = 0, 0
Free Energy = -15.18
..(((((((.......(((((((((((((((................)))))))))))))))..........)))))))..
model uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
..(({{(((.......{[[{(((((((((((................)))))))))))}]]}......-...)))}}))..
target GGUUACACUGCUUCCUUGACGUCUUAGCUCGGAACCUCCAUGUGAAGUGAGCUAAGACCGAUGCUCUU-UCAAGUCAGAGC
**** ^^ ****