_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:1     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: e-115
 Query name: gi|825310506|gb|AKJ23337.1| deiodinase 2b [Salmo salar]
 Query range: 1-268  (total 268)

 Target: /data/www-rg/seblastian_results/803861140/tempfiles/temptarget.fasta
 Chromosome: CM007959.1:subseq_76359543,104522_ Strand: +
 Positions:
 -Exon 1  50000        50221
 -Exon 2  53941        54525

 Redox box: no

Query   MGAASVDLLVTLQILPGFFSNCLFLALYDSVVLVKRVVSLLSCPGGGGGEWQRMLTSAGLRSIWNSFLLDAYKQ <---Intron---> VKLGSEAPNS
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <   3719bp   > ||||||||||
Target  MGAASVDLLVTLQILPGFFSNCLFLALYDSVVLVKRVVSLLSCPGGGGGEWQRMLTSAGLRSIWNSFLLDAYKQ                VKLGSEAPNS
        agggaggccgaccaccgtttatctcgctgtggcgacggttcatcggggggtccacatggcctataatccggtac                gacgaggcat
        tgccgtatttctattcgttcagtttctaacttttagttcttggcgggggagagttcccgtgctgagtttacaaa                tatggaccac
        gctccgcggcccgcggtcccccgccgcccggggggtgggggcctcccgagggcggcgagctcagcctggcacag                gatctgaccc
                                                                                                            

Query   KVVKVPGSGGNHGFRRRSSV-TTTARHPGDECRLLDFESSERPLVVNFGSATUPPFISHLPAFRRLVEEFSNVADFLLVYIDEAHPSDGWVAPTMGPCSF
        ||||||||||||| |||||| ||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Target  KVVKVPGSGGNHGVRRRSSVTTTTARHPGDECRLLDFESSERPLVVNFGSATUPPFISHLPAFRLLVEEFSNVADFLLVYIDEAHPSDGWVAPTMGPCSF
        aggagcgaggacggccaaagaaaagcccgggtcccgtgttgcccggatgtgatcctaacccgtcccgggttagggtccgtagggcctggtggcaagcttt
        attatcggggaagtgggggtcccccgacgaaggttataccagctttatgcccgccttgatcctgtttaatcatcattttataacaccaggtccctgcgct
        agggtttcttctccgggctgcccgctttacgccgactgaagcttggcctgccacaccccgtccggggggctcgtccggccccggccaccgggccgcaccc
                                                            *                                               

Query   EVRKHRSLEERVVAAMKLTEAFSLPPQCQLVADCMDNNANVAYGVSYERVCIVQRRKIAYLGGKGPFFYNLKDVRQYLEQRYGKR
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  EVRKHRSLEERVVAAMKLTEAFSLPPQCQLVADCMDNNANVAYGVSYERVCIVQRRKIAYLGGKGPFFYNLKDVRQYLEQRYGKR
        ggaacctcggaggggaacaggtacccctccgggtagaagaggtggttgagtagcaaaagtcggagctttacaggactcgcatgaa
        atgaagctaagttcctatcactgtccagattcagtaaacatcagtcaagtgttaggatcatggagcttaataatgaataagagag
        gcggcgggaggggtcgagtgcccggtgcgggtccgccttcacccgccgggccggaggtccgtgaacccccggtgggtgagatcga
                                                                                             
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 1913 ; UGA-SECIS: 2309

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007959.1:subseq_76359543,104522_ Strand = + Positions = 56439 - 56523
 Found by:  Infernal (score=21.56) Covels (score=20.49)
 Stem2 length = 9   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -16.8

         ..(((((((.........(((((((((((((((...................)))))))))))))))..........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccuggcccuAAAcC----cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ..(((({(((........{[[[((((({{((((...................))))}})))))]]]}......-..)))}))))..
 target  ACGGGGCUGGUGUGAGAAUGAAAACCACUGACUAAAGGGGGGUAACUAACUCAGUCUUUGGUUGGAUGACAGA-CCUCACCUCCUU
                           ****           ^^^                           ****