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

 Blastx evalue: 2e-21
 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/356114657/tempfiles/temptarget.fasta
 Chromosome: WARS01000032.1:subseq_4102030,200000_:subseq_0,120000_ Strand: +
 Positions:
 -Exon 1  98959        99098
 -Exon 2  100056       100166
 -Exon 3  102182       102308
 -Exon 4  103805       103892
 -Exon 5  104185       104300

 Redox box: YES

Query   MVMKWLRFTFLALGLFSLCCSSAGDSSGIKKMKMQFATGPLLKFQIC <---Intron---> ISUGYKRVFEEYTQALYQRYPDIRIEGENYLPIPIYR
        | ||||||/ | ||||||||/|/|||||/|||||||||||||||||| <   957bp    > ||||||||||||||||||||||||||||||||||/||
Target  MAMKWLRFSLLVLGLFSLCCASSGDSSGVKKMKMQFATGPLLKFQIC                ISUGYKRVFEEYTQALYQRYPDIRIEGENYLPIPLYR
        agaattcttccgtgcttcttgttggaaggaaaaactgagcccatcat                attgtacgtggtacgttcctcgacagggatccacctc
        tctagtgtcttttgttctggcccgagggtaatatatccgcttatatg                tcggaagttaaacactaagacatgtagaaatctctag
        gggggattgccaggtcggcccgttccccgggggggttgacccatac                ctcagcgggtggcggcgcggcaccctaggctttatct 
                                                                         *                                  

Query    <---Intron---> HIASFLSVFKLLVIGLIIIGRDPFALFGMQAPGIWEWGQGNK <---Intron---> IYACMMVFFFSNMIENQLMSTGAFEI
         <   2015bp   > |/|||||/|||||||/|||||||||||||||||||||||||| <   1496bp   > ||||||||| ||||||||||||||||
Target                  HVASFLSIFKLLVIGVIIIGRDPFALFGMQAPGIWEWGQGNK                IYACMMVFFLSNMIENQLMSTGAFEI
                        cggttctataccgaggaaagagctgctgacgcgatgtgcgaa                atgtaagttcaaaagactataggtga
                        atccttcttattttgttttggactcttgtaccgtgaggagaa                tacgttttttgattaaattccgctat
                       acctccgtacggggtggttacgcatccttgacaccgggcgatg                atccgggcccctgtacgagcgagtac
                                                                                                            

Query   TLND <---Intron---> VPVWSKLESGHLPSMQQLVQILDNEMKMNVHMNTRPHH
        |||| <   292bp    > ||||||||||||||||||||||||||||||||||||||
Target  TLND                VPVWSKLESGHLPSMQQLVQILDNEMKMNVHMNTRPHH
        atag                gcgttacgtgccctacccgcacgagaaaagcaaaaccc
        cta                atctgcatacgatcctaattattaaatatatatacgcaa
        aat                tgaggaaagatcgccgggtaacgccggggcacgcaaact
                                                                  
 Sequence until next stop: 
TCCTAA
 S  * 

 Distance CDS-SECIS: 161 ; UGA-SECIS: 593

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = WARS01000032.1:subseq_4102030,200000_:subseq_0,120000_ Strand = + Positions = 104462 - 104536
 Found by:  Infernal (score=38.39) Covels (score=32.92)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -19.99

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .({(((((((--....{[[[(((((({((((................))))}))))))]]]}..--...)))))))}).
 target  UGAAGUGAUG--UUAAUGAAGGUCUGCGCUGAAGGCAGGAAAACUGCUAGCACAGACUGGAUGC--CCCCAUCACUCUU
                         ****           ^^                         ****