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

 Blastx evalue: 0.0
 Query name: gi|984143962|ref|XP_015332391.1| PREDICTED: thyroxine 5-deiodinase [Marmota marmota marmota]
 Query range: 1-303  (total 303)

 Target: /data/www-rg/seblastian_results/201928528/tempfiles/temptarget.fasta
 Chromosome: KZ295204.1:subseq_525733,50791_ Strand: -
 Positions:
 -Exon 1  25000        25905

 Redox box: no

Query   MPRQAASRLVVGEGEGPPGASGPTATMLRSLLLHSLRLCAQTASCLVLFPRFLGTAFMLWLLDFLCIRKHFLGRRRRQPEPEVELNSEGEEVPPDDPPIC
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||
Target  MPRQAASRLVVGEGEGPPGASGPTATMLRSLLLHSLRLCAQTASCLVLFPRFLGTAFMLWLLDFLCIRKHFLG-RRRQPEPEVELNSEGEEVPPDDPPIC
        acccggtctgggggggccggtgcagaacctcccctcactgcagttcgctcctcgagtactccgtctacactcg-cccccgcgggcaagggggccggccat
        tcgacccgtttgagagccgccgccccttgctttactgtgcacccgttttcgttgcctttgttattgtgaattg-gggacacatatagagaatccaacctg
        gtcgccggggcaacggcggcggcgccgcccggtccggctcgccgccgccgccacgccgcgccccgcccgtcgc-cccgcacaggcttgcgggccccaccc
                                                                                                            

Query   VSDDNRLCTLASLKAVWHGQKLDFFKQAHEGGPAPNSEVVLPEGFRSQRILDYAQGNRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEA
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  VSDDNRLCTLASLKAVWHGQKLDFFKQAHEGGPAPNSEVVLPEGFRSQRILDYAQGNRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEA
        gtggacctacgtcaggtcgcatgttacgcgggcgcatgggccggtcaccacgtgcgacccgcatgatatcctagcaagtcccgaatccgggtcaataggg
        tcaaagtgctcctactgagaatattaacaaggcccacatttcagtggagttaacagagctttatgggcgccttcgtgctagttcaaagatattttataac
        gcccccgccgggcgcggtcgggtccggacgcaagccgggcgtgccgcgccactcagcaaggctcccccaagcggcgcccgtgccgcgcccctcccctgaa
                                                                            *                               

Query   HPSDGWITTDSPYIIPQHRSLEDRVSAARVLQQGAPGCALVLDTMANSSSSAYGAYFERLYVIQSGTIMYQGGRGPDGYQVSELRTWLERYDEQLHGTRP
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Target  HPSDGWITTDSPYIIPQHRSLEDRVSAARVLQQGAPGCALVLDTMANSSSSAYGAYFERLYVIQSGTIMYQGGRGPDGYQVSELRTWLERYDEQLHGIRP
        cctggtaaagtctaaccccacggcgaggagcccggcgtgcgcgaagataatgtggttgcctgacagaaatcggcgcggtcgtgccatcgctggctcgacc
        accaggtccaccattcaaggtaagtgccgttaagccggctttactcacggccagcatagtattaggcttaaggggcagaatcatgcgtagaaaatagtgc
        ttcccgccaccgcctcacgcggcgccaaggggatgaccagcgccgctcccgatccccgcccccgttccgcgactcatccgcaggctgggcttgggcctgc
                                                                                                            

Query   RRL
        |||
Target  RRL
        cct
        ggt
        tgg
           
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 533 ; UGA-SECIS: 935

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KZ295204.1:subseq_525733,50791_ Strand = - Positions = 24466 - 24386
 Found by:  Infernal (score=18.93) Covels (score=28.11)
 Stem2 length = 8   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -14.4

         ..(((((((..........(((((((((((((((...............))))))))))))))).........)))))))..
 model   uucggucaugcg---UuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ...((((((..........([[{(({((({(((.................)))})))}))}]]).....-...))))))...
 target  GCGCGAGCCCCACUGCUGAUGACGAACUAUCUCUAACUGGUCUUGACCACGAGCUGGCUCCGAACUGCA-GGAGGCUCGAAA
                            ****           ^^                        ****