_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | 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/457853449/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: + Positions: -Exon 1 48329 48398 -Exon 2 50004 50069 -Exon 3 53321 53377 -Exon 4 53496 53637 -Exon 5 53986 54060 -Exon 6 54678 54756 -Exon 7 55171 55233 -Exon 8 56099 56169 -Exon 9 62295 62314 -Exon 10 62918 63009 -Exon 11 64116 64290 -Exon 12 70254 70390 -Exon 13 71416 71511 -Exon 14 71891 71983 -Exon 15 73197 73268 -Exon 16 73338 73435 -Exon 17 74077 74203 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 = 75052 - 75120 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 **** ^^^ ****