_________________________________.______________________._________________________________________________________________________________ _|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:1 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: 1e-31 Query name: gi|929438980|ref|XP_005481982.2| PREDICTED: selenoprotein O [Zonotrichia albicollis] Query range: 1-583 (total 583) Target: /data/www-rg/seblastian_results/462148196/tempfiles/temptarget.fasta Chromosome: your_sequence Strand: - Positions: -Exon 1 59844 60112 -Exon 2 58360 58563 -Exon 3 57253 57433 -Exon 4 54688 54818 -Exon 5 54043 54323 -Exon 6 53547 53697 -Exon 7 51593 51778 -Exon 8 50003 50159 -Exon 9 49136 49327 Redox box: YES Query MSLPALALLGLEAPAADPEEAEAEAALFFSGNRVPAGAEPAAHCYCGHQFGSFAGQLGDGAAMYLGEVLGPRGERWEIQLKGAGITPFSR <---Intro |||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 1280b Target MSLPALALLGLEAPAADPAAAEAEAALFFSGNRVPAGAEPAAHCYCGHQFGSFAGQLGDGAAMYLGEVLGPRGERWEIQLKGAGITPFSR atccgcgccgcggcgggcggggggggcttagacgcggggcggctttgcctgatggccgggggatcgggcgccggctgaccagggaacttc tctcctcttgtaccccaccccacacctttggagtccgcacccagaggaatggtcgatgagcctatgattgcggaggatatagcgtcctcg gggggggggggggcgccgggcgngcggcccgcggggcggtgtccccgcgccccggggcccccgcgcgggcggcgcggcgcgcccccctc Query n---> QADGRKVLRSSIREFLCSEAMFHLGIPTTRAGTCVTSDSRVLRDIFYDGNPKHERCTVVLRIASTFIR <---Intron---> FGSFEIFKPP p > ||||||||||||||||||||||||||||||||||||||||||||| ||||||/||||||||||||||| < 926bp > |||||| ||| Target QADGRKVLRSSIREFLCSEAMFHLGIPTTRAGTCVTSDSRVLRDIXYDGNPKNERCTVVLRIASTFIR FGSFEIXKPP cgggcagcctaacgtctaggatccgacaacggatgatgtagccgattggacaagataggcaagtataa tgttgatacc acaggattgcgtgattggacttatgtcccgcgcgtccacgttgatnaagacaaaggctttgtcccttg tgctattacc ggntgggggggccggcgccgcgccgaacatctcccgacccactgccttcgcaatagtactggactata gtcttatngct Query DEYTGRKGPSVNRNDIRIQMLDYVISTFYPEIQEAHSGNTVQRNAAFFKE <---Intron---> VTRRTARLVAEWQCVGFCHGVLNTDNMSIVGLTI |||||||||||||||||||||||||||||||||||/| |||||||||||| < 2434bp > /|/||||||||||||||||||||||||||||||| Target DEYTGRKGPSVNRNDIRIQMLDYVISTFYPEIQEAYSDNTVQRNAAFFKE ITKRTARLVAEWQCVGFCHGVLNTDNMSIVGLTI ggtagcagcagacagacacacgtgaaattcgacggttgaagcaaggttag aaacagacgggtctggttcggcaagaaaaggtaa aaacggagcgtagaatgtattaattgctacataacacaactagaccttaa tcagccgttcagagtgtgagttacaatgttgtct tacaacgcccgcctctgaggtttgcctccaacggttaccttggtttccag ccgcagggtggggcggtctcggtatcgtttaact Query DYGPFGFMDR <---Intron---> YDPEHVCNGSDNTGRYAYNKQPEICKWNLGKLAEALVPELPLEISQLILEEEYDAEFEKHYLQKMRKKLGLIQL |||||||||| < 364bp > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Target DYGPFGFMDR YDPEHVCNGSDNTGRYAYNKQPEICKWNLGKLAEALVPELPLEISQLILEEEYDAEFEKHYLQKMRKKLGLIQL gtgctgtaga tgcgcgtagtgaagctgtaaccgatatacgacgggtgcgcctgaaccacgggtgggtgacttcaaaaacgcacc aagctgttag aacaatgagcaacggacaaaacatgagatgatcacttcatctatgatttaaaaacataaaataatgaatgttat ctcttctgc gtctgcgcttttcagcttccagagtcggcggattatataggcgaacaccgagattaatgactggggaaaacacag Query ELEEDSKLVSELLETMHLTA <---Intron---> GDFTNIFYLLSSFSVDIDPSKFEDFLEELTSQCASVEELKVVFKPQMDPR <---Intron--- |||||||||||||||||||| < 345bp > ||||||||||||||||||||||||||| |||||||||||||||||||||| < 1768bp Target ELEEDSKLVSELLETMHLTA GDFTNIFYLLSSFSVDIDPSKFEDFLEXLTSQCASVEELKVVFKPQMDPR gtgggaacgtgccgaaccag ggtaaatttcatttggagctatggttggcaactgtgggcaggtaccagca ataaagattcattactatc cgatcattattgctctataccataattaatcgagcctaatatttacatacg aaaatcgggtagtacgtca taccatttcggtacaactttaataccaantatgtttgaggatttaaggta Query > QLSMMLMLAQSNPQLLALIGTKANINKELERIEQFSKLQQLTADDLLSRNKRHWKEWLEKYR <---Intron---> VRLQKEIESVGNADAWNTER > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 1433bp > ||||||||||||| |||||| Target QLSMMLMLAQSNPQLLALIGTKANINKELERIEQFSKLQQLTADDLLSRNKRHWKEWLEKYR VRLQKEIESVGNAAAWNTER cctaacatgctaccctgtagaagaaaagcgcagcttaccctagggtcaaaaactagtcgata gctcagagaggagggtaagc atctttttcacacattcttgcacataaatagtaatcataatccaattggaagagaagtaaag tgtaaatagtgacccgacag aggagggggtgtttggaaatacattataggactagctagggaaattatcataacggaggggc actggaaaattttttcgctgt Query VKVMNSNNPKYILRNYIAQNAIEAAENGDFSE <---Intron---> VRKVLKLLEHPFQEAEGFQEVKEDAEEEGA-AAAAACSQESRSKQSYCSKPP |||||||||||||||||||||||||||||||| < 675bp > || ||||||||||||||||||||||||||| | |||||||/||||||||||| Target VKVMNSNNPKYILRNYIAQNAIEAAENGDFSE VRNVLKLLEHPFQEAEGFQEVKEDAEEEGATATAAACSQETRSKQSYCSKPP gagaataacatataatagcagaggggaggttg gaagcactgcctcggggtcggaggggggggagagggttcgaaaactttaacc tattacaacaattgaatcaactaccaagatca tgattattaactaacagtaataaacaaagcccccccgcaacggaacaggacc cgcgtactaatcggtttcgtcaaatatatcag aacagataatacaaaatcgaaggtaaggaattaattttggcacaactccatg Query LWASELCVTUSS |||||||||||| Target LWASELCVTUSS ctgtgctgattt tgccatgtcgcc ggtggcctgata * Sequence until next stop: TAA * Distance CDS-SECIS: 322 ; UGA-SECIS: 328 ------- SECIS element -- id:1 -- grade:A ---- Chromosome = your_sequence Strand = - Positions = 48813 - 48736 Found by: Infernal (score=23.45) Covels (score=27.52) Stem2 length = 11 Apical loop length = 17 Insertion in stem2 = 0, 0 Free Energy = -8.55 ..(((((((.......(((((((((((((((.................))))))))))))))).........))))))).. model uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc ..(((((((.--....{[[((((((((((((.................))))))))))))]]}.....-...))))))).. target GAGUUGUUGU--UAUGUGAAGACAAAAAUAGCAAGUCAGGAAUCUGAUCUGUUUUUGUCUGAUGUCUU-AACUAAUAGUAC **** ^^ ****