_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 9e-25 Query name: gi|27807131|ref|NP_777051.1| thioredoxin reductase 2, mitochondrial precursor [Bos taurus] >gi|190359067|sp|Q9N2I8.2|TRXR2_BOVIN RecName: Full=Thioredoxin reductase 2, mitochondrial; AltName: Full=Thioredoxin reductase TR3; Flags: Precursor >gi|5360756|dbj|BAA82153.1| thioredoxin reductase [Bos taurus] Query range: 1-511 (total 511) Target: /data/www-rg/seblastian_results/546645207/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: + Positions: -Exon 1 45009 45078 -Exon 2 46684 46749 -Exon 3 50001 50057 -Exon 4 50176 50317 -Exon 5 50666 50740 -Exon 6 51358 51436 -Exon 7 51851 51913 -Exon 8 52779 52849 -Exon 9 58975 58994 -Exon 10 59598 59689 -Exon 11 60796 60970 -Exon 12 66934 67070 -Exon 13 68096 68191 -Exon 14 68571 68663 -Exon 15 69877 69948 -Exon 16 70018 70115 -Exon 17 70757 70883 Redox box: no Query MAALRGAAARFRGRAPGGARGAAG <---Intron---> RQCYDLLVIGGGSGGLACAKEA <---Intron---> AQLGKKVAVLDYVEPSPQG <- ||||||||||| |||||||||||| < 1605bp > || ||||||||||||||||||| < 3251bp > |||||||||||||||||/| < Target MAALRGAAARFPGRAPGGARGAAG RQRYDLLVIGGGSGGLACAKEA AQLGKKVAVLDYVEPSPRG aggccggggctcgcgcgggcgggg ccctgccgagggtggcgtgagg gccgaagggcgtggctccg tcctggcccgtcggccggcggcc ggagaattttgggcggtcgcaa ccatgaatcttaatacccg ggggcagcgtcgccggcgggcca cgagtccggcctacccgcccga tcggggggcggccggtcca Query --Intron---> TRWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAPHYGWGVAQAPHSW <---Intron---> ATLADAVQNHVKSLNWGHRIQLQD 118bp > |||||||||||||||||||||||||||||||||||||| |||||| | < 348bp > ||/||||||||||||||||/|||| Target TRWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAPHYGWRVAQAPHDW ATMADAVQNHVKSLNWGHRVQLQD aatgcggatgaggtacaacaccggccggaacggcctgtcggcgccgt gaaggggcacgatcatgccgcccg gcgggtggcgtatggtcaattaaccttggttgaccaagggtcaccaag cctcactaaatactaggagtataa ccggccccccgtcccccggggcggggggcgccccccccgcgcgcacc gaaggtccgccggcgcgccccgggc Query R <---Intron---> KVKYFNVKASFVDTHTVCGVSKGGEE <---Intron---> TLLSAEHIVIATGGRPRYPTH <---Intron---> IEGA | < 617bp > |||| ||||||||||||||||||||| < 414bp > ||||||||||||||||||||| < 865bp > |||| Target R KVKYLNVKASFVDTHTVCGVSKGGEE TLLSAEHIVIATGGRPRYPTH IEGA a agattagagatggacagtggtagggg acctggcagagaggccctcac aggg g ataatatacgttacactggtcaggaa cttccaatttccgggcgacca tagc gacgtgccgcctccgcgtctccatggg tgtgcgctctccatgggccgc catc Query LEYGITSDDLFWLKESPGKT <---Intron---> LVVGASY <---Intron---> VALECAGLLTGLGLDTTVMIRSVPLRAFDQ <---Intron |||||||||||||||||||| < 6125bp > ||||||| < 603bp > ||||||| |||||||||||||||||||||| < 1106bp Target LEYGITSDDLFWLKESPGKT LVVGASY VALECAGFLTGLGLDTTVMIRSVPLRAFDQ tgtgaaaggcttcagtcgaa tggggat ggcgtggtcagcgtgaagaacagcccgtgc taagtcgaattgtaaccgac tttgcg atctagcgttcgtgtacctttggtctgctaa gacgcgctcccgggactga gggcgcc cacggcgccccgccgccccgaccgccgcccg Query ---> QMASLVTEHMAGHGTRILRGCAPEKVEKLPGQQLRVTWVDLTSDRKDAGTFDTVLWAIG <---Intron---> RVPETASLNLEKAGVHTNPV > ||| ||||||||||||/|||||||/|||||||||||||||| ||||||||||||||||| < 5963bp > ||||||||||||||| |||| Target QMALLVTEHMAGHGTRVLRGCAPERVEKLPGQQLRVTWVDLASDRKDAGTFDTVLWAIG RVPETASLNLEKAGVRTNPV cagtcgagcaggcgacgccgtgcgaggaccgccccgatggcgtgcagggatgagctgag cgcgagacatgagggcaacg atctttcaatcgagcgttgggccagtaatcgaatgtcgtatccagaacgctacttgct ggtcaccgtataacgtgcact agtgtccgcgtccccgcggccccgggggcacggccccggctcgcggtgcctccgcgca cataacgtgtgagttgtgccc Query TGKILVDAQETTSVPHIYAIGDVAE <---Intron---> GRPELTPTAIMAGRLLAQRLSGRTSDLMDYSS <---Intron---> VPTTVFTPLEY |||| ||||| ||/||||||||||| < 1025bp > |||||||||||||||||||||||||||||||| < 379bp > ||||||||||| Target TGKIFVDAQEATSIPHIYAIGDVAE GRPELTPTAIMAGRLLAQRLSGRTSDLMDYSS VPTTVFTPLEY agaatgggcggataccatgaggggg gccgcacagaaggcccgcccagcatgcagtaa gcaagtaccgt cgatttacaaccctcatactgatca ggcatccccttcggttcagtgggccattaagg tcccttcctaa tggccttcgaccccccccccccgag gggggacaccgcggcgcgggccgcacggcccc ccgtcctcggt Query GCVGLSEEAAVARHGEEHVE <---Intron---> VYHAFYKPLEFTVPQRDASQCYIK <---Intron---> MVCLREPPQLVLGLHFLGPNAGEV |||||||||||||||||||| < 1213bp > ||||||||||||||||||||||/| < 69bp > |||||||||||||||||||||||| Target GCVGLSEEAAVARHGEEHVE VYHAFYKPLEFTVPQRDASQCYVK MVCLREPPQLVLGLHFLGPNAGEV gtggctggggggccgggcgg gtcgttaccgtagcccggtcttga agtccgccccgcgcctcgcagggg ggtgtcaacctcgagaaata taactaactatctcagaccagata ttgtgaccatttgtattgcacgat ccgggaggacgtctaagcgg tctgctagggctccggtatgccag ggtgggcaggggcgccccccacat Query IQGFALGIK <---Intron---> CGASYQQLMRTVGIHPTCAEEVAKLRISKRSGLDPTVTGCUG |||||||| < 641bp > ||||/||//||||||||||||||||||||||||||||||||| Target TQGFALGIK CGASFQQVIRTVGIHPTCAEEVAKLRISKRSGLDPTVTGCUG acgtgcgaa tggttccgacaggaccatgggggaccatactgcgcagagttg cagtctgta ggcctaattgctgtaccgcaatcatgtcagcgtacctcgggg tggtcggc gtgcccgggacggccccctggggcgccccgcccgccggcccac * Sequence until next stop: TAG * Distance CDS-SECIS: 848 ; UGA-SECIS: 851 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = your_sequence Strand = + Positions = 71732 - 71800 Found by: Infernal (score=28.41) Covels (score=33.92) Stem2 length = 9 Apical loop length = 14 Insertion in stem2 = 0, 0 Free Energy = -20.94 Type = 1 ..(((((((.......(((((((((((((((...............)))))))))))))))........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc ...((((((---....([[(((({(({((((.....-.........))))}))}))))]])----..-.))))))... target CGCCGCCAG---AUGAUGAGGACCUGUGCGGAAACC-CCCCGCGGGCUGCCCAUGUCUGAG----CC-CCUGGCGUGA **** ^^^ ****