_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:QUE_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 3e-35 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/352210157/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: + Positions: -Exon 1 39528 39650 -Exon 2 45104 45164 -Exon 3 46764 46873 -Exon 4 47056 47172 -Exon 5 49052 49124 -Exon 6 50001 50120 -Exon 7 50521 50663 -Exon 8 52066 52181 -Exon 9 52289 52514 -Exon 10 52732 52824 -Exon 11 53243 53319 -Exon 12 53852 54008 -Exon 13 54215 54322 -Exon 14 55205 55300 -Exon 15 55508 55642 -Exon 16 55771 55836 Redox box: no Query PPPPGQTRLPDWDGLKLRVRTLIASHRVMIFSKSYCPYCNK <---Intron---> VKELFNSLHVEYYALELDVID <---Intron---> DGASIQ |||| ||||||||||||||| |||||||||||||||||||| < 5453bp > |||||/||||/|||||||| | < 1599bp > |||||| Target PPPPVQTRLPDWDGLKLRVRNLIASHRVMIFSKSYCPYCNK VKELFHSLHVDYYALELDVTD DGASIQ ccccgcacccgtggcaccgcacagtccgaataaattcttaa gagctctccggttgcgcggag gggaac cccctacgtcagagtatgtgattccagttttgagagcagaa taattactataaactatatc aagcgta ggggagcgcgcgcgggccggccccgcccgcccgcccccccg ggacccagtgccttgggtat ctacttg Query QVLAELTNQRTVPNVFVNGTHIGGCDATFQ <---Intron---> AYKDGSLQKLLGDNQ-ITEPYEYDLIIIGGGSGGLACSK <---Intron---> ||| ||||||||||||||||||||||||/| < 182bp > ||||||||||||||| ||||||||||||||||||||||| < 1879bp > Target QVLVELTNQRTVPNVFVNGTHIGGCDATYQ AYKDGSLQKLLGDNQTITEPYEYDLIIIGGGSGGLACSK cgtggcaacaagcagtgagacaggtggatc gtaggtccaccggacaaagctgtgcaaagggtggcgtta atttatcaagctcatttagcatgggaccaa caaagctaattgaaactcacaaaattttgggcggtcgca aagaggtcggagttatgtatcttcttaacg ttgtaaggactgtcactaactattctttttcagatgttg Query EAAALGKKVMVLDYVVPTPLGTSWG <---Intron---> LGGTCVNVGCIPKKLMHQAALLGQALQDSRKYGWQYEEQV <---Intron---> KH ||||||||||||||||||||||||| < 876bp > |||||||||||||||||||||||||||||||||||||||| < 400bp > || Target EAAALGKKVMVLDYVVPTPLGTSWG LGGTCVNVGCIPKKLMHQAALLGQALQDSRKYGWQYEEQV KH ggggtgaagagtgtggcaccgattg cggatgaggtacaacaccggccgcgccgtaatgtctggcg ac accctgaattttaattccctgccg gtggcgtatggtcaattaaccttgactaacgaaggaaaaa taa attcgagaagaactttaattacag attcgtatatctcggggtaaatgtaacataggtgggtaaa tac Query NWETMVEAIQNYIGSLNWGYRVSLREKSVTYLNSYGEFVEPHKIK <---Intron---> ATNRKGQVTYHTAETFVVATGERPRYLGIPGDKEFCITS ||||||||/||||||| |||||||||||||||||||||||||||| < 1402bp > |||||||||||||||||/||||||||||||||||||||| Target NWETMVEAVQNYIGSLXWGYRVSLREKSVTYLNSYGEFVEPHKIK ATNRKGQVTYHTAETFVLATGERPRYLGIPGDKEFCITS atgaaggggcatagtcatgtcgttagatgatcattggtggccaaa gaaaagcgatcaggatgcgaggacatcgacggagttaaa agacttactaaatgctaggagtctgaactcatacagattacaata ccagagatcaaccactttccgagcgatgtcgaaatgtcg cggcggaatgcctttangctagtgaggtgacctttaacgaacacg atcagaaactcaagttggtaaggaatgtctataaccta Query <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAEKVGAYMETHGVKFIRKFVPVQ <---Intr < 107bp > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 217b Target DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAEKVGAYMETHGVKFIRKFVPVQ ggcttccttcgaacggggttggcgtggtcggcgcggagagctacccgtgcgaggagggtagacggataaatgcgc aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgcatacagtattgattcta ttccccgtcctcgtgtgttccgtggtagtgtcgggtctggctcttggctcaagaagnaccgaaccggccggtattg Query on---> VEQLEQGMPGRLKVTAKSTEGPETLEEEYNT <---Intron---> VLLAVGRDACTRNIGLQTIGVKINEK <---Intron---> NGKV p > ||||||||||||||||||||| ||||||||| < 418bp > ||||/||||||||||||||||||||| < 532bp > |||| Target VEQLEQGMPGRLKVTAKSTEGSETLEEEYNT VLLAIGRDACTRNIGLQTIGVKINEK NGKV ggccgcgacgacagagataggtgacgggtaa gtcgagcggtaaaagtcaaggaaaga agag taataagtcggtatccaccagcactaaaaac tttctggacgcgatgtactgtataaa agat tggggaagaaagagaagttgagactaaatcc tgacttttttcgtttggattcactg gtgac Query PVNDEERTNVPYVYAIGDILDGKLELTPVAIQAGRLLAQRLYGGSSKK <---Intron---> CDYINVPTTVFTPLEYGSCGYPEEKAISEYGEQNLE ||||| /||||||||||||||||||||||||||||||||||||||||| < 206bp > |||||||||||||||||||||||/||| |||||||| Target PVNDEXQTNVPYVYAIGDILDGKLELTPVAIQAGRLLAQRLYGGSSKK CDYINVPTTVFTPLEYGSCGYPEQKAIDEYGEQNLE cgagggcaagctgtgaggatggacgcacggacggaccgcactggataa tgtaagcaagtactgtgatgtcgcagaggtggcatg ctaaaaacatcatactgattagatatcctctacggttcagtagggcaa gaatatcccttcctaaggggacaaactaaagaaata tattanactgttttatgtcgtagtattatctgagaggcaggtgttcag tctctaaaagtctagtcctgttaaacatatagacgg Query <---Intron---> VYHTLFWPLEWTVPGRDNNTCYAKIICNKQDN <---Intron---> NRVIGLHVLGPNAGEVTQGFAAAIKCGLTKELLDET < 882bp > ||||||||||||||||||||||||/||||||| < 207bp > ||||||||||||||||||||||||||||||||||| Target VYHTLFWPLEWTVPGRDNNTCYAKVICNKQDN XRVIGLHVLGPNAGEVTQGFAAAIKCGLTKELLDET gtcatttccgtagcgagaaattgagataacga acgagccgcgcaggggacgtgggaatgcaagtcgga taacttgctagctcggaaacgacattgaaaaa agttgtattgcacgatcagtccctaggtcaattaac ttctgcgatagagccatctcttagtcctagct ntgaagtttactttataattttacattccaaattaa Query IGIHPTCAE <---Intron---> VFTTMDITKSSGQDITQKGCUG ||||||||| < 128bp > |||||||||||||||||||||| Target IGIHPTCAE VFTTMDITKSSGQDITQKGCUG agaccatgg gtaaagaaattgcgaacagttg tgtaccgca ttcctatcaccgaatcaagggg ttcttttag gctagttcattcgcctggccat * Sequence until next stop: TAA * Distance CDS-SECIS: 214 ; UGA-SECIS: 217 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = your_sequence Strand = + Positions = 56051 - 56142 Found by: Infernal (score=31.13) Covels (score=24.32) Stem2 length = 10 Apical loop length = 16 Insertion in stem2 = 0, 0 Free Energy = -24.26 ..(((((((......................(((((((((((((((................)))))))))))))))........))))))).. model uucggucaugcg---------------UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc ((((((((((.....................{[[{((((({(((((................)))))})))))}]]}..--...)))))))))) target CUUUGCCUGGAUUAGCGCUGCGGUGCUUUCUUGACGUUGUUGCUCAAAAUCUCCUUGUGAGGUGAGCUGCGACUGAUGU--CUGCCAGGCAAGG **** ^^^ ****