_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| | knownSP | secis_index:2 SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_ _________________________________|______________________|_________________________________________________________________________________ Blastx evalue: e-134 Query name: gi|927115335|ref|XP_013919774.1| PREDICTED: type II iodothyronine deiodinase isoform X1 [Thamnophis sirtalis] Query range: 1-280 (total 280) Target: /data/www-rg/seblastian_results/445288548/tempfiles/temptarget.fasta Chromosome: ULFR01000002.1:subseq_46215341,115161_ Strand: - Positions: -Exon 1 64940 65161 -Exon 2 49955 50572 Redox box: no Query MGLLSIDLLITLQILPVFFSNCLFLALYDSVVLLKHMVLLLSCSKAARGEWRRMLTSEGLRCVWNSFLLDAYKQ <---Intron---> VKLGGDAPNS |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 14367bp > |||||/|||| Target MGLLSIDLLITLQILPVFFSNCLFLALYDSVVLLKHMVLLLSCSKAARGEWRRMLTSEGLRCVWNSFLLDAYKQ VKLGGEAPNS agttaagctaaccaccgtttatctcgctgtggctacagcccattaggcggtcaacatggtctgtaatccggtac gatggggcat tgttgtatttctattctttcagtttctaacttttaatttttggcaccggagggttccagtggtgagtttacaaa tatggaccac gcgactcggcatgcggttcccctcccctcggccggcggttgtccgtatcagaggcaagcacccgtctcatccag gagtaatttc Query NVIHIPNGTAESSSNCRWKSSMGKYGSECHLLDFAKSDRPLVINFGSATUPPFTNQLSAFGKLVEEFSSVADFLLVYIDEAHPSDGWAAPGISSSFEVKK |||||||||||||||||||||||||||||||||||||/|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Target NVIHIPNGTAESSSNCRWKSSMGKYGSECHLLDFAKSERPLVINFGSATUPPFTNQLSAFGKLVEEFSSVADFLLVYIDEAHPSDGWAAPGISSSFEVKK agacacagaggaaaatataatagatgagtcctgtgatgcccgaatgtgatcctaacctgtgatgggttagggtctgtagggcctggtggcgattttggaa attatcagccagggagggagctgaaggagattatcacagctttatgcccgcctcaatcctgattaatcgtcattttataacaccaggcccgtccctataa ctccatttttacccccagaccgaatatactcactcaagcatacctgatcatccacggtctcgggagcttgtctgaccttgtcaatcgttttcatatacga * Query HRNQEDRCAAAHQLLKKFSLPPQCQIVADCMDNNANVAYGVSFERVCIIQRQKIAYLGGKGPFFYNLQEVRLWLEQNFRKRUNPNVPDKNSRGLSF |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/||| |||||| Target HRNQEDRCAAAHQLLKKFSLPPQCQIVADCMDNNANVAYGVSFERVCIIQRQKIAYLGGKGPFFYNLQEVRLWLEQNFRKRUNPNLPDKKSRGLSF caacggatgggccccaatttccctcagggtagaagaggtggttgcgtaacacaagtcggagctttaccggcctcgcataaatacatcgaatagctt agaaaaggcccaattaatctccagattcagtaaacatcagtctagtgttagaatcatggagcttaataatgtgtaaatgaggacatcaaacggtct tgcaacattttcgtagattgaagcgagttcgcttctgttacctgtactaaaaattcgggacttccttagtatgggaccgaaatataatggaaagct * Sequence until next stop: TAA * Distance CDS-SECIS: 1338 ; UGA-SECIS: 1380 ------- SECIS element -- id:2 -- grade:B ---- Chromosome = ULFR01000002.1:subseq_46215341,115161_ Strand = - Positions = 48616 - 48539 Found by: Infernal (score=14.25) Covels (score=15.13) Stem2 length = 11 Apical loop length = 14 Insertion in stem2 = 0, 0 Free Energy = -9.38 ..(((((((............((((((((((.(((((...............))))).))))))))))........))))))).. model uucggucaugcg-----UuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggc-caggcCuGAUGuuuuuucaugaccggc ..(({((((............([[({(((((((((((.....-.........)))))))))))})]])----.--.))))})).. target GGAUCACAUAAGGAACAAUCAUGAGAACAUUACCUUGCAUUC-UUUCUGCACUGAGGUAAUGUCUGAG----C--AAUGUAAUGA **** ****