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

 Blastx evalue: 2e-16
 Query name: gi|929071820|ref|XP_014045606.1| PREDICTED: selenoprotein T1a-like [Salmo salar]
 Query range: 1-169  (total 196)

 Target: /data/www-rg/seblastian_results/529694289/tempfiles/temptarget.fasta
 Chromosome: CM007942.1:subseq_50378102,102205_ Strand: +
 Positions:
 -Exon 1  49991        50127
 -Exon 2  50835        50945
 -Exon 3  51292        51418
 -Exon 4  51960        52047
 -Exon 5  52165        52205

 Redox box: YES

Query   MAERWLPFSIIFLGVLSLYCAASADNSGIKKMKMQFATGPLLKFQIC <---Intron---> ISUGYKRVFEEYMQALYQRYPDIRIEGENYLPLPLYR
        ||/||||||//|| ||||||||||||||/|||||||||||||||||| <   707bp    > |||||||||||||| ||||||||||||||||||||||
Target  MAKRWLPFSLLFL-VLSLYCAASADNSGLKKMKMQFATGPLLKFQIC                ISUGYKRVFEEYMQVLYQRYPDIRIEGENYLPLPLYR
        agaatccttcctc-gctcttggtggaagcaaaaactgagcccatcat                attgtacgtggtacgttcctcgacagggatccccctc
        tcaggtctctttt-ttctagccccaaggtaatatatccgcttatatg                tcggaagttaaatattaagacatgtagaaatctctag
        gggggactgcgta-tccgcttggttcccggaggggtaagattacac                cccagcgggtggcggcgcgtcaccctgggccttaccc 
                                                                         *                                  

Query    <---Intron---> HVASFLSMFKLALIGLIIIGKDPFALCGMQAPGIWVWGQENK <---Intron---> IYACMMVFFFSNMIENQCMSTGAFEI
         <   346bp    > |||||||||||||||||||||||||||||||||||||||||| <   541bp    > ||||||||||||||||||||||||||
Target                  HVASFLSMFKLALIGLIIIGKDPFALCGMQAPGIWVWGQENK                IYACMMVFFFSNMIENQCMSTGAFEI
                        cggttctatatgcagcaaagagctgctgacgcgatgtgcgaa                atgtaagtttaaaagactataggtga
                        atccttcttatcttgttttgaactctggtaccgtgtggaaaa                tacgttttttgattaaagtccgctat
                       ccttccgcgcggagcagctccgcccccctgacaccgcgtggtg                ttccggactcccgtacgcgaaattac
                                                                                                            

Query   TLND <---Intron---> VPVWSKLESGHLP
        |||| <   117bp    > |||||||||||||
Target  TLND                VPVWSKLESGHLP
        atag                gcgttacgtgccc
        cta                atctgcatacgatc
        aac                tgaggcggggtcgc
                                         
 Sequence until next stop: 
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTCTATTCACATGACCATAGTTGTCAAATTAGATTACTCAACCTACTCAACTTGTTTTTTTTACAAAACTTCAAGGACTTCATTTATTTATGCGCTTGATGTACTCACTTTTCTGTCTCCCTTTCTTTTCCTCTGCAGGTTTGAGGTGGGTTTCTCAATGGACTGTGAGGTGATGTTTATGAAGGTCTGCTCTGAAGGCAGGAAGACTGCTAGCTCAGACTGGATGTCCCCATCGCTTCTCACCACGTCCCTACGAGATGCCCCTCCCCTAATGCTGGACTGGGATCCATGGCAACCGTGA
 X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  X  S  I  H  M  T  I  V  V  K  L  D  Y  S  T  Y  S  T  C  F  F  Y  K  T  S  R  T  S  F  I  Y  A  L  D  V  L  T  F  L  S  P  F  L  F  L  C  R  F  E  V  G  F  S  M  D  C  E  V  M  F  M  K  V  C  S  E  G  R  K  T  A  S  S  D  W  M  S  P  S  L  L  T  T  S  L  R  D  A  P  P  L  M  L  D  W  D  P  W  Q  P  * 

 Distance CDS-SECIS: 665 ; UGA-SECIS: 1022

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007942.1:subseq_50378102,102205_ Strand = + Positions = 52871 - 52945
 Found by:  Infernal (score=26.2) Covels (score=28.71)
 Stem2 length = 9   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -20.59

         ..(((((((.......((((((((((.(((((................))))).))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcC-cuuuuuggggcgggc-caggcCuGAUGuuuuuucaugaccggc
         .(((((((((--....{[[[(((((({-{(((................)))}-}))))))]]]}..--...))))))))).
 target  UGAGGUGAUG--UUUAUGAAGGUCUGC-UCUGAAGGCAGGAAGACUGCUAGC-UCAGACUGGAUGU--CCCCAUCGCUUCU
                         ****            ^^                          ****