_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:QUE_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 3e-56 Query name: gi|385648265|ref|NP_001245307.1| thioredoxin reductase 3 [Taeniopygia guttata] Query range: 2-607 (total 607) Target: /data/www-rg/seblastian_results/344423402/tempfiles/temptarget.fasta Chromosome: CM003722.1:subseq_10163722,106596_ Strand: + Positions: -Exon 1 40625 40747 -Exon 2 46154 46214 -Exon 3 47788 47897 -Exon 4 48068 48181 -Exon 5 49976 50048 -Exon 6 50892 51011 -Exon 7 51399 51541 -Exon 8 52929 53044 -Exon 9 53152 53377 -Exon 10 53629 53721 -Exon 11 54163 54239 -Exon 12 54789 54945 -Exon 13 55148 55255 -Exon 14 56139 56234 -Exon 15 56441 56575 -Exon 16 56707 56772 Redox box: no Query PPPPGQTRLPDWDGLKLRVRTLIASHRVMIFSKSYCPYCNK <---Intron---> VKELFNSLHVEYYALELDVID <---Intron---> DGASIQ |||||||||||||||||||||||||||||||||/||||||| < 5406bp > ||||| |/ ||||||||| | < 1573bp > |||||| Target PPPPGQTRLPDWDGLKLRVRTLIASHRVMIFSKNYCPYCNK VKELFRSIGVEYYALELDATD DGASIQ ccccgcacccgtggcaccgcacagtccgaataaattcttaa gagctctagggttgcgcggag gggaac ccccgacgtcagagtatgtgcttccagttttgaaagcagaa taattgctgtaaactatacc aagcgta ggggagcgcgcgcgggccggtcccccccgcccgccctcccg ggaccccctggctcgagtat ttacttg Query QVLAELTNQRTVPNVFVNGTHIGGCDATFQ <---Intron---> AYKDGSLQKLLGDNQITEPYEYDLIIIGGGSGGLACSK <---Intron---> ||| ||||||||||||||||||||||||/| < 170bp > ||/||||||||||||||||||||||||||||||||||| < 1794bp > Target QVLVELTNQRTVPNVFVNGTHIGGCDATYQ AYQDGSLQKLLGDNQITEPYEYDLIIIGGGSGGLACSK cgtggcaacaagcagtgagacaggtggatc gtcggtccaccggacaagctgtgcaaagggtggcgtta atttatcaagctcatttagcatgggaccaa caaagctaattgaaatcacaaaattttgggcggtcgca aagaggccggagttatgtatcttcttagtg ttgtaaggactgccataactattctttttcatatattg Query EAAALGKKVMVLDYVVPTPLGTSWG <---Intron---> LGGTCVNVGCIPKKLMHQAALLGQALQDSRKYGWQYEEQV <---Intron---> KHN ||| ||||||||||||||||||||| < 843bp > |||||||||||||||||||||||||||||||||||||||| < 387bp > ||| Target EAATLGKKVMVLDYVVPTPLGTSWG LGGTCVNVGCIPKKLMHQAALLGQALQDSRKYGWQYEEQV KHN gggatgaagagtgtggcaccgattg cggatgaggtacaacaccggccgcgccgtaatgtctggcg aca accctgaattttaattccctgccg gtggcgtatggtcaattaaccttgactaacgaaggaaaaa taaa attcgggaagaattttaattacag attcgtatatcttggggtaaatgtgacgtaggtgggtaaa tacc Query WETMVEAIQNYIGSLNWGYRVSLREKSVTYLNSYGEFVEPHKIK <---Intron---> ATNRKGQVTYHTAETFVVATGERPRYLGIPGDKEFCITS || ||||||||||||||||||||||||||||||||||||||||| < 1387bp > |||||||||||||||||/||||||||||||||||||||| Target WEIMVEAIQNYIGSLNWGYRVSLREKSVTYLNSYGEFVEPHKIK ATNRKGQVTYHTAETFVLATGERPRYLGIPGDKEFCITS tgaagggacatagttatgtcgtcagatgatcattggtggccaaa gaaaagcgatcaggatgcgaggacatcgacggagttaaa gatttactaaatgctaggagtctgaactcatacagattacaata ccagagatcaaccactttccgagcgatgtcgaaatgtcg gacgaaatgcctttacgatagcgaggtgacctttcgtgaacatg atcaaaaactcaagttcgaaaagaacgtctataaccta Query <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAEKVGAYMETHGVKFIRKFVPVQ <---Intro < 107bp > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 251bp Target DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAEKVGAYMETHGVKFIRKFVPVQ ggcttccttcgaacggggttggcgtggtcggcgcggagagctacccgtgcgaggagggtagacggataaatgcgc aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgcatacagtattgattcta ttcgccgtcctcgtgtgttttatggtagtgtcgtgtcagggtcctggttcgagaaactccgagctggtcgatattg Query n---> VEQLEQGMPGRLKVTAKSTEGPETLEEEYNT <---Intron---> VLLAVGRDACTRNIGLQTIGVKINEK <---Intron---> NGKVP > ||||||||||||||||||||| | ||||| < 441bp > ||||/||||||||||||||||||||| < 549bp > ||||| Target VEQLEQGMPGRLKVTAKSTEGSEIFAEEYNT VLLAIGRDACTRNIGLQTIGVKINEK NGKVP ggccgcgacgacagagataggtgatgggtaa gttgagcggtaaaagtcaaggaaaga agagc taataagtcggtatccaccagcattcaaaac tttctggacgcgatgtactgtataaa agatc tggagaagaaagagaagttgaaactaaatct tgacttttatcgtttagactcactg gtgact Query VNDEERTNVPYVYAIGDILDGKLELTPVAIQAGRLLAQRLYGGSSKK <---Intron---> CDYINVPTTVFTPLEYGSCGYPEEKAISEYGEQNLE |||||/|||||||||||||||||||||||||||||||||||||||/| < 202bp > ||||||||||||||||||||||||||/ |||/|||| Target VNDEEQTNVPYVYAIGDILDGKLELTPVAIQAGRLLAQRLYGGSSRK CDYINVPTTVFTPLEYGSCGYPEEKAMEEYGKQNLE gagggcaagctgtgaggatggacgcacggacggaccgcactggataa tgtaagcaagtactgtgatgtcggagaggtgacatg taaaaacatcatactgattagatatcctctacggttcagtagggcga gaatatcccttcctaaggggacaaactaaagaaata attaaaccgttttatgtcgtagtattatctgagaggcaggtgttcag tctctaaaagtctagtcctgttaaacgaatggacgg Query <---Intron---> VYHTLFWPLEWTVPGRDNNTCYAKIICNKQDN <---Intron---> NRVIGLHVLGPNAGEVTQGFAAAIKCGLTKELLDETI < 883bp > ||||||||||||| |||||||||||||||||| < 206bp > ||||||||||||||||||||||||||||||||||||| Target VYHTLFWPLEWTVAGRDNNTCYAKIICNKQDN NRVIGLHVLGPNAGEVTQGFAAAIKCGLTKELLDETI gtcatttccgtagggagaaattgaaataacga acgagccgcgcaggggacgtgggaatgcaagtcggaa taacttgctagctcggaaacgacattgaaaaa agttgtattgcacgatcagtccctaggtcaattaact ttctacgatagagacatctcttagtcctagct ttgaggtttactttatcattttacgttccaaattaat Query GIHPTCAE <---Intron---> VFTTMDITKSSGQDITQKGCUG |||||||| < 131bp > |||||||||||||||||||||| Target GIHPTCAE VFTTMDITKSSGQDITQKGCUG gaccatgg gtaaagaaattgcgaacagttg gtaccgca ttcctatcaccgaatcaagggg tctcttag actagttcattaacctggccat * Sequence until next stop: TAA * Distance CDS-SECIS: 215 ; UGA-SECIS: 218 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = CM003722.1:subseq_10163722,106596_ Strand = + Positions = 56988 - 57080 Found by: Infernal (score=29.64) Covels (score=25.0) Stem2 length = 11 Apical loop length = 16 Insertion in stem2 = 0, 0 Free Energy = -28.39 ..(((((((.......................(((((((((((((((................)))))))))))))))........))))))).. model uucggucaugcg----------------UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc ((((((((((((....................{[[{(((((((((((................)))))))))))}]]}..--.)))))))))))) target CUUUGCUUGGCAUUAGCACUGCGGUGCUUCUUUGACGUUGUAGCUCAGAACCUUCUCACCAGGUGAGCUACGACUGAUGG--CUGCCAGGCAAGG **** ^^ ****