_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:QUE_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 2e-58 Query name: gi|385648265|ref|NP_001245307.1| thioredoxin reductase 3 [Taeniopygia guttata] Query range: 1-607 (total 607) Target: /data/www-rg/seblastian_results/429535395/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: - Positions: -Exon 1 65853 65978 -Exon 2 60353 60413 -Exon 3 58655 58764 -Exon 4 58359 58472 -Exon 5 56489 56561 -Exon 6 55502 55621 -Exon 7 54952 55094 -Exon 8 53426 53541 -Exon 9 53089 53314 -Exon 10 52779 52871 -Exon 11 52291 52367 -Exon 12 51595 51751 -Exon 13 51324 51431 -Exon 14 50343 50438 -Exon 15 50003 50137 -Exon 16 49806 49871 Redox box: no Query MPPPPGQTRLPDWDGLKLRVRTLIASHRVMIFSKSYCPYCNK <---Intron---> VKELFNSLHVEYYALELDVID <---Intron---> DGASI | |||||||||||||||||||||||||||||||||||||||| < 5439bp > ||||| || |||||||||| | < 1588bp > ||||| Target MAPPPGQTRLPDWDGLKLRVRTLIASHRVMIFSKSYCPYCNK VKELFRSLRVEYYALELDVAD DGASI agcccgcacccgtggcaccgcacagtccgaataaattcttaa gagctctccggttgcgcgggg gggaa tccccgacgtcagagtatgtgcttccagttttgagagcagaa taattgctgtaaactatatc aagcgt gggggagcgcgcgcgggccggccccgcccgcccgcccacccg ggaccccgtggcttgagtat ctactt Query QQVLAELTNQRTVPNVFVNGTHIGGCDATFQ <---Intron---> AYKDGSLQKLLGDNQITEPYEYDLIIIGGGSGGLACSK <---Intron---> ||||||||||||||||||||||/||||||/| < 182bp > |||||||||||||||||||||||||||||||||||||| < 1797bp > Target QQVLAELTNQRTVPNVFVNGTHVGGCDATYQ AYKDGSLQKLLGDNQITEPYEYDLIIIGGGSGGLACSK ccgtggcaacaagcagtgagacgggtggatc gtaggtccaccggacaagctgtgcaaagggtggcgtta aattcatcaagctcatttagcatgggaccaa caaagctaattgaaatcacaaaattttgggcggtcgca gaagaggccggagttatgtatcttcttaatg ttgtaaggactgtcatagctattctttttcatatattg Query EAAALGKKVMVLDYVVPTPLGTSWG <---Intron---> LGGTCVNVGCIPKKLMHQAALLGQALQDSRKYGWQYEEQV <---Intron---> KH ||||||||||||||||||||||||| < 867bp > |||||||||||||||||||||||||||||||||||||||| < 407bp > || Target EAAALGKKVMVLDYVVPTPLGTSWG LGGTCVNVGCIPKKLMHQAALLGQALQDSRKYGWQYEEQV KH ggggtgaagagtgtggcaccgattg cggatgaggtacaacaccggccgcgccgtaatgtctggcg ac accctgaattttaattccctgccg gtggcgtatggtcaattaaccttgactaacgaaggaaaaa taa attcgagaagaattttaattacag attcgtatatctcggggtaaatgtgacataggtgggtaaa tac Query NWETMVEAIQNYIGSLNWGYRVSLREKSVTYLNSYGEFVEPHKIK <---Intron---> ATNRKGQVTYHTAETFVVATGERPRYLGIPGDKEFCITS ||||||||/|||||||||||||||||||||||||||||||||||| < 1410bp > |||||||||||||||||/|||||||| |||||||||||| Target NWETMVEAVQNYIGSLNWGYRVSLREKSVTYLNSYGEFVEPHKIK ATNRKGQVTYHTAETFVLATGERPRYPGIPGDKEFCITS atgaaggggcatagtcatgtcgttagatgatcattggtggccaaa gaaaagcgatcaggatgcgaggacatcgacggagttaaa agacttactaaatgctaggagtctgaactcatacagattacaata ccagagatcaaccactttccgagcgacgtcgaaatgtcg cggcgaaatgcctttacgctagtgaggtgacctttaacgaacacg atcaaaaactcaagttggtaaagaacatctataacctc Query <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAEKVGAYMETHGVKFIRKFVPVQ <---Intr < 111bp > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 217b Target DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQEMAEKVGAYMETHGVKFIRKFVPVQ ggcttccttcgaacggggttggcgtggtcggcgcggagagctacccgtgcgaggagggtagacggataaatgcgc aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgcatacagtattgattcta ttccccgtcctcgtgtgttccgtggtagtgtcgtgtccgggtctgggttcaagaaactccgaactggccggtattg Query on---> VEQLEQGMPGRLKVTAKSTEGPETLEEEYNT <---Intron---> VLLAVGRDACTRNIGLQTIGVKINEK <---Intron---> NGKV p > ||||||||||||||||||||||/ ||||||| < 411bp > ||/|/||||||||||||||||||||| < 539bp > |||| Target VEQLEQGMPGRLKVTAKSTEGPKILEEEYNT VLIAIGRDACTRNIGLQTIGVKINEK NGKV ggccgcgacgacagagataggcaacgggtaa gtagagcggtaaaagtcaaggaaaga agag taataagtcggtatccaccagcattaaaaac tttctggacgcgatgtactgtataaa agat tggggaagaaagagaggttgaaactaaatct tgacttttatcgtttagattcactg gtgac Query PVNDEERTNVPYVYAIGDILDGKLELTPVAIQAGRLLAQRLYGGSSKK <---Intron---> CDYINVPTTVFTPLEYGSCGYPEEKAISEYGEQNLE ||||||/|||||||||||||/||||||||||||||||||||||||||| < 163bp > ||||||||||||||||||||||||||| |||||||| Target PVNDEEQTNVPYVYAIGDILEGKLELTPVAIQAGRLLAQRLYGGSSKK CDYINVPTTVFTPLEYGSCGYPEEKAIDEYGEQNLE cgagggcaagctgtgaggatggacgcacggacggaccgcactggataa tgtaagcaagtactgtgatgtcggagaggtggcatg ctaaaaacatcatactgattagatatcctctacggttcagtagggcaa gaatatcccttcctaaggggacaaactaaagaaata tattaaactgttttatgtcgaagtattatctgagaggcaggtgttcag tctctaaaagtctagtcctgttaaacatatagacgg Query <---Intron---> VYHTLFWPLEWTVPGRDNNTCYAKIICNKQDN <---Intron---> NRVIGLHVLGPNAGEVTQGFAAAIKCGLTKELLDET < 885bp > |||||||||||||||||||||||||||||||| < 205bp > |||||||||||||||||||||||||||||||||||| Target VYHTLFWPLEWTVPGRDNNTCYAKIICNKQDN NRVIGLHVLGPNAGEVTQGFAAAIKCGLTKELLDET gtcatttccgtagcgagaaattgaaataacga acgagccgcgcaggggacgtgggaatgcaagtcgga taacttgctagctcggaaacgacattgaaaaa agttgtattgcacgatcagtccctaggtcaattaac ttccgcgatagagccgtctcttagccctagct ttgaagtttactttatcattttacattccaaattaa Query IGIHPTCAE <---Intron---> VFTTMDITKSSGQDITQKGCUG ||||||||| < 131bp > |||||||||||||||||||||| Target IGIHPTCAE VFTTMDITKSSGQDITQKGCUG agaccatgg gtaaagaaattgcgaacagttg tgtaccgca ttcctatcaccgaatcaagggg ctcttttag gctggttcattggcctggccat * Sequence until next stop: TAA * Distance CDS-SECIS: 229 ; UGA-SECIS: 232 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = your_sequence Strand = - Positions = 49576 - 49500 Found by: Infernal (score=30.6) Covels (score=26.25) Stem2 length = 10 Apical loop length = 16 Insertion in stem2 = 0, 0 Free Energy = -12.39 ..(((((((.......(((((((((((((((................)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc ..(([{{{((......{[[{((((({(((((................)))))})))))}]]}..--...))}}}])).. target CACUGCGGUGCUUUCUUGACGUUGUUGCUCAAAAUCUUCUUGUGAGGUGAGCUACGACUGAUGC--UGCCAGGCAAGGC **** ^^^ ****