_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 7e-23 Query name: gi|755469480|gb|AHB30480.2| thioredoxin reductase 3 [Oplegnathus fasciatus] Query range: 36-602 (total 602) Target: /data/www-rg/seblastian_results/87578157/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: + Positions: -Exon 1 58788 58860 -Exon 2 59759 59868 -Exon 3 62522 62626 -Exon 4 62840 62912 -Exon 5 63807 63922 -Exon 6 66379 66497 -Exon 7 67097 67322 -Exon 8 68011 68103 -Exon 9 74585 74661 -Exon 10 75397 75553 -Exon 11 76166 76273 -Exon 12 80901 80996 -Exon 13 84642 84776 -Exon 14 84916 84981 Redox box: no Query FCVKVKDLFKELKVECNVVELDLIE <---Intron---> DGTNYQEMLLEMTGQKTVPNVFINKTHIGGCDKTLQ <---Intron---> AHKDGSL | //||/|| | |/||//||| / < 898bp > /| / ||/| ||| |/|||//|/|/ |/|||| | | < 2653bp > ||/ | | Target FSLQVKELFSSLGVDCNILELDQAD EGASVQEVLSEMTNQRTVPSIFVNRVHVGGCDHTFQ AHQSGLL tttcgagctttcgggtaatgcgcgg gggagcggctgaaacaagcaatgaagcgggtgcatc gccagtt tctataattcctgtagattataac aagcgtaattcatcaagctcgtttagtatgggaacta caaggtt taggtaactttgatctccgattat tggctcggtaaggccggtgccctgtagcgcttcctcg atgttaa Query QQLLSGENEAYDYDLIVIGGGSGGLACSK <---Intron---> EAALLGKKAMVLDYVVPTPKGTTWG <---Intron---> LGGTCVNVGCIPKK |||| // ||||||||||||||||/|// < 213bp > |||/||/| ||||/|||/|/|| || < 894bp > |||||||||||||| Target QQLLQ-QDLAYDYDLIVIGGGSGGLSCAQ EAAVLGRKVMVLDFVVPSPRGTAWG LGGTCVNVGCIPKK ccccc-cgcgtgtgcagagggtggcttgc ggggcgaagagcgtggctccgagtg cggatgaggtacaa aatta-aatcaaaattttgggcggtcgca accttggattttatttcccggccg gtggcgtatggtcaa ggccg-gcggcccccccccgccgccgctg acccggggcgtgccgcaccccgcg tttcgtgttctcggg Query LMHQTALLGTAMQDARKFGWEFDE <---Intron---> TVKHNWETMKMAVNNYIGSLNWGYRVALRDKNVNYVNAYAEFIEPHKIKAINKRGKETFY |||| |||| |/ |/||||||/ / < 2456bp > || |//|/| | Target LMHQAALLGQALTDSRKFGWEYSQ ------------------------------------------------KATNEKGQEALY caccggccgcgcagtaatgtgtac ------------------------------------------------agaagagcggct ttaaccttgactcacgatggaaga ------------------------------------------------accaaagaacta ggcgtggaggggcccggccggctg ------------------------------------------------gactgaagggtc Query TAAKFVLATGERPRYLGIPGDKEYCITS <---Intron---> DDLFSLSYCPGKTLVIGASYVALECGGFLAGLGLDVTVMVRSILLRGFDQDMANRA ||||||/|||/||||||||||/|||||| < 599bp > |||||| |||| |||/||||||||| ||||||||/|||||||/|||||||/|| / Target TAAKFVIATGQRPRYLGIPGDREYCITS DDLFSLPYCPGTTLVVGASYVALECAGFLAGLGLEVTVMVRSVLLRGFDQEMAEKV aggatgagagcaccttgacggagttaaa ggcttccttcgaacggggttggcgtggtcggcgcggagagctgcccgtgcgaggag cccatttccgagcgatgtcgagaagtcg aattctcagcgcctttgccatctagcgttcgtgtatctttgctttggtaaatcaat ttggtccgaagggccgacgacagcccc cccgcggcccgcgcgggcgccggggtaccgccgcggcacggcggcggcccgggcggg Query GEHMEEHGVKFLRKYVPVK <---Intron---> VEELEAGTPGRLKVTAKSTETDEIIEGEYNT <---Intron---> VLIAVGRDACTDKIGLDK | /// ||/||||/|||/ < 688bp > |//|| | |||||| ||||| | /|| ||| < 6481bp > ||/|/|||/|| |/||/| Target GACLQQLGVRFLRKFVPVE VQQLEKGLPGRLKVVAKSTEGTETMEGVYNT VLLAIGRDSCTKKLGLEK ggtccccggctccatgcgg gcccgagccgacagggataggagaagggtaa gttgagcgttaaatgcga gcgtaatgtgttgattcta taataagtcggtattcaccagcactagtaac tttctggacgcaatgtaa cccgggccgccgcgcgcgg cgggggcgcggggcgtacgagagaggctccg tgaatttcccgggagggg Query TGVKVNPK <---Intron---> NGKIPVNDEEQTNVPHIYAIGDILEGKWELTPVAIQAGKLLARRLYGGSKLK <---Intron---> CDYVNVPT || // | < 735bp > |||||| ||||/||//||/||/|||| /|||||//|||||||||/|| | < 612bp > |||||||| Target IGVNISEK TGKIPVNGEEQTSVPYVYAVGDVLEGKPQLTPVAVRAGKLLARRLFGGRSEK CDYVNVPT aggaaaga agaacgagggcaagctgtgggggcggacccacgggcggaccgcactggctga tgtgagca tgtatgaa cgatctagaaacgtcatactgattagacatcctctgcgattcggttgggcaa gaatatcc ttgtctg ggcgcaatcgggctgctcctcgccggcgggccgccgggcggggagttgcaagg tccccccc Query TVFTPLEYGACGLSEERATELYGKDNIE <---Intron---> VFHSLFWPLEFTVPNRDNNKCYGKIICNKLDS <---Intron---> DRVIGFHY |||||||| || |||/| |/ /|/ < 4627bp > |/|/||||||/|| |||| || ||||||||/ < 3645bp > ||||||| Target VVFTPLEYGCCGYSEEKAGEVCQAENLG VYHTLFWPLEWTVACRDNNTCYAKIICNKLDN DRVIGFHV ggtactgtgttgttggaggggtcggacg gtcacttccgtaggtagaaattgaaataacga gcgagtcg tttcctaaggggacaaacgatgacaatg taacttgctagctcggaaacgacattgaataa agttgtat ggcgcggccctgcagggtcggcgggtgt ccccgcgtcggagccaccctccggacctagcc tggaatcc Query LGPNAGEVTQGFGAAMKCGATKEQLDSTIGIHPTCAE <---Intron---> IFTTLEVTKSSGGDITQAGCUG |||||||/|||| |||||| ||/ ||/|||||||| | < 139bp > /|||||/||/|| |||| |||| Target LGPNAGEITQGFAAAMKCGLTKQLLDATIGIHPTCGE VFTTLEITKASGLDITQKGCUG cgcagggaacgtgggaatgcaacccggaagaccatgg gtaatgaaagtgcgaacagttg tgcacgatcagtccctaggtcaattacctgtaccgga ttcctatcaccgtatcaagggg cagccggctggtctcggtgcaggggtcccgcccgtag gcccggccgggagccgggccac * Sequence until next stop: TAG * Distance CDS-SECIS: 137 ; UGA-SECIS: 140 ------- SECIS element -- id:1 -- grade:B ---- Chromosome = your_sequence Strand = + Positions = 85119 - 85189 Found by: Infernal (score=17.61) Covels (score=12.55) Stem2 length = 10 Apical loop length = 11 Insertion in stem2 = 0, 0 Free Energy = -14.7 Type = 1 ..(((((((.......(((((((((((((((................))))))))))))))).........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc ...(((({(---....{[[{((((({(((((.........-----..)))))})))))}]]}.....-...)}))))... target CUCGCUGCC---UCCUUGACGUCUUCGCUCAGAGCCGCCA-----GGUGAGCCAAGACCGACCUCUG-CCCGCCAGCUCC **** ^^ ****