_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:2     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
_________________________________|______________________|_________________________________________________________________________________

 Blastx evalue: e-144
 Query name: gi|825310551|gb|AKJ23338.1| deiodinase 3a1 [Salmo salar]
 Query range: 1-266  (total 266)

 Target: /data/www-rg/seblastian_results/413261608/tempfiles/temptarget.fasta
 Chromosome: CM007942.1:subseq_30995337,100773_ Strand: +
 Positions:
 -Exon 1  50000        50797

 Redox box: no

Query   MQKSAGVLTVLALKHTALCLVLLPRFLLAALMLCLLDVLCIRRKVLLKMEGSSPEDPPVCVSDSNKMFTLESLRAVWYGQKLDFFKSAHIGLIAPNTEVV
        ||||||||||||||||||||/||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||/||||||||||
Target  MQKSAGVLTVLALKHTALCLILLPRFLLAALMLCLLDVLCIRRKVLLKMEGSSPEDPPVCVSDSNKMFTLESLRAVWYGQKLDFFKSAHLGLIAPNTEVV
        acatgggcagcgcacagctcacccctccggcactccggctaaaagccaaggaacggccgtgtgtaaatacgtcaggttgcatgttatgccgcagcaaggg
        taaccgttcttctaacctgttttcgtttcctttgttattgtggatttatagggcaacctgtcacaattctactgctgagaatattaccatgttccacatt
        gggtatcggggcgacatatgtggcgccgaggggtcgccgtcggaggggggccccacgtcccccccggccgggcgcggcggaactcacgctatcgcctgtg
                                                                                                            

Query   QLQERRRVRVLDYVKGRRPLILNFGSCSUPPFMTRLAAFQRVASQYADIADSLLVYIEEAHPSDGWVSSDAPYQIPKHCCLEDRLKAAQLMHSEVPCCNV
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| /|
Target  QLQERRRVRVLDYVKGRRPLILNFGSCSUPPFMTRLAAFQRVASQYADIADSLLVYIEEAHPSDGWVSSDAPYQIPKHCCLEDRLKAAQLMHSEVPCSSV
        cccgccagagcgtgagaaccacatgatttcctaaccggtccggactggaggtccgtagggcctggtgatggctcacacttcggacaggccactggctaag
        ataagggtgttaatagggctttatgggcgccttcgtcctagtcgaacatcactttataacaccaggtgcaccaatcaaggtaagtaccattacatcgggt
        gggggcgcgcactgaggatcccccctccaagcggcgtgtgccgcgtgcccccgtatcgggtcgccggcccgacgccgcctggcagactgggcggtccctg
                                    *                                                                       

Query   VVDTMDNSSNAAYGAYFERLYILRDERVVYQGGRGPEGYRISELRNWLEQYRNDLENSSRTVVVHV
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Target  VVDTMDNSSNAAYGAYFERLYILRDERVVYQGGRGPEGYRISELRNWLEQYRNDLENSSRTVVVHV
        gggaagattaggtggttgactacaggcggtcggagcggtcatgcaatcgctcagtgataaagggcg
        ttactaaccaccagcatagtattgaagttaaggggcagagtcatgagtaaagaataacggctttat
        ggttgccgccgtcacttgattcggtggcgtggcgaggccgaagtgcgcgacgttggtccaaggcct
                                                                          
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 1110 ; UGA-SECIS: 1521

------- SECIS element -- id:2 -- grade:A ----
 Chromosome = CM007942.1:subseq_30995337,100773_ Strand = + Positions = 51908 - 51989
 Found by:  Infernal (score=22.08) Covels (score=26.04)
 Stem2 length = 11   Apical loop length = 16   Insertion in stem2 = 0, 1
 Free Energy = -20.39

         ..(((((((.......(((((((((((((((................))))))))).))))))...........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccagg-cCuGAUGuu--u-uuucaugaccggc
         (((((((((((((...{[[((((((((((((................))))))))).)))]]}......)-))))))))))))
 target  UACUCUAGUGUUGUUGUGAAGUUCGGUUUUUAAAGGGUUUUAAACCAGGAAACUGAUACUGAUGUUGUUU-GAUACUAGAGUA
                         ****           ^^^                         ****