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

 Blastx evalue: 2e-19
 Query name: gi|1035264199|ref|XP_008332202.2| PREDICTED: selenoprotein T1a-like [Cynoglossus semilaevis]
 Query range: 1-194  (total 196)

 Target: /data/www-rg/seblastian_results/224723258/tempfiles/temptarget.fasta
 Chromosome: JXSJ01000006.1:subseq_6104489,103645_ Strand: -
 Positions:
 -Exon 1  53512        53651
 -Exon 2  52485        52595
 -Exon 3  51309        51435
 -Exon 4  50180        50267
 -Exon 5  49952        50067

 Redox box: YES

Query   MVMKWLRFTFLALGLFSLCCSSAGDSSGIKKMKMQFATGPLLKFQIC <---Intron---> ISUGYKRVFEEYTQALYQRYPDIRIEGENYLPIPIYR
        | |/||||/ ||||||||||///|||||/|||||||||||||||||| <   916bp    > ||||||||||||||||||||||||||||||||||/||
Target  MAMRWLRFSLLALGLFSLCCATSGDSSGVKKMKMQFATGPLLKFQIC                ISUGYKRVFEEYTQALYQRYPDIRIEGENYLPIPLYR
        agaattcttccgtgcttcttgatggaaggaaaaactgagcccatcat                attgtacgtggtacgttcctcgacagggatccacctc
        tctggtgtcttctgttctggcccgagggtaatatatccgcttatatg                tcggaagttaaacactaagacatgtagaaatctctag
        ggggggttgccgggccgacccgttccccgggggggtggacccgtat                ctcagcgggtggcggcgcggcgccctaggctttacct 
                                                                         *                                  

Query    <---Intron---> HIASFLSVFKLLVIGLIIIGRDPFALFGMQAPGIWEWGQGNK <---Intron---> IYACMMVFFFSNMIENQLMSTGAFEI
         <   1049bp   > |||||||/|||||||/||||/||||||||||||||||||||| <   1041bp   > ||||||||| ||||||||||||||||
Target                  HIASFLSMFKLLVIGVIIIGKDPFALFGMQAPGIWEWGQGNK                IYACMMVFFLSNMIENQLMSTGAFEI
                        cagttctataccgaggaaagagctgctgacgcgatgtgcgaa                atgtaagttcaaaagactataggtga
                        atccttcttattttgttttgaactcttgtaccgtgaggagaa                tacgttttttgattaaattccgctat
                       acttccgtgcagggtggttccgcacccttgacgccgggcgatg                atccgggctcctgtacgagtagttac
                                                                                                            

Query   TLND <---Intron---> VPVWSKLESGHLPSMQQLVQILDNEMKMNVHMNTRPHH
        |||| <   112bp    > ||||||||||||||||||||||||||||||||||/|||
Target  TLND                VPVWSKLESGHLPSMQQLVQILDNEMKMNVHMNTKPHH
        atag                gcgttacgtgccctacccgcacgagaaaagcaaaaccc
        cta                atctgcatacgatcctaattattaaatatatatacacaa
        aac                tgaggaaggatccccgggtgacgccggggctcgcaaacc
                                                                  
 Sequence until next stop: 
TCCTAA
 S  * 

 Distance CDS-SECIS: 195 ; UGA-SECIS: 627

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JXSJ01000006.1:subseq_6104489,103645_ Strand = - Positions = 49756 - 49684
 Found by:  Infernal (score=33.44) Covels (score=33.17)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -19.09

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...((((((---....{[[[(((((({((((................))))}))))))]]]}..--..-.))))))...
 target  GAAGUGAUG---UUUAUGAAGGUCUGCGCUGAAGGCAGGAAGACUGCUAGCACAGACUGGAUGC--CC-CCAUCACCCU
                         ****           ^^                         ****