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

 Blastx evalue: 9e-20
 Query name: gi|1035264199|ref|XP_008332202.2| PREDICTED: selenoprotein T1a-like [Cynoglossus semilaevis]
 Query range: 1-196  (total 196)

 Target: /data/www-rg/seblastian_results/431197318/tempfiles/temptarget.fasta
 Chromosome: KV884716.1:subseq_1091911,100000_ Strand: -
 Positions:
 -Exon 1  51574        51713
 -Exon 2  49888        49998
 -Exon 3  46881        47007
 -Exon 4  45466        45553
 -Exon 5  45075        45196

 Redox box: YES

Query   MVMKWLRFTFLALGLFSLCCSSAGDSSGIKKMKMQFATGPLLKFQIC <---Intron---> ISUGYKRVFEEYTQALYQRYPDIRIEGENYLPIPIYR
        | ||||||/|| ||/ ||||///|||/ ||||||||||||||||||| <   1575bp   > ||||||||||||||||||||||||||||||||/||||
Target  MAMKWLRFSFLVLGVLSLCCATSGDSNSIKKMKMQFATGPLLKFQIC                ISUGYKRVFEEYTQALYQRYPDIRIEGENYLPMPIYR
        agaatcctttcgcggtttttgatggaaaaaaaaactgagcccatcat                attgtacgtggtacgttcctcgacagggatccacatc
        tctagtgtcttttgttctggcccgagagtaatatatccgcttatatg                tcggaagttaaacactaagacatgtagaaatctctag
        ggggggttccccggtgagctcatttcccagaggggttgaatcatat                cccagcgggtggcggcgcggcaccctaggctctgcct 
                                                                         *                                  

Query    <---Intron---> HIASFLSVFKLLVIGLIIIGRDPFALFGMQAPGIWEWGQGNK <---Intron---> IYACMMVFFFSNMIENQLMSTGAFEI
         <   2880bp   > |||| ||/||||||||/|/|/|||||||||||||||||| || <   1327bp   > ||||||||||||||||||||||||||
Target                  HIASILSIFKLLVIGLVIVGKDPFALFGMQAPGIWEWGQANK                IYACMMVFFFSNMIENQLMSTGAFEI
                        cagtactataccgagcgaggagctgctgacgcgatgtgcgaa                atgtaagtttaaaagactataggtga
                        atccttcttattttgttttgaactcttgtaccgtgaggacaa                tacgttttttgattaaattccgctat
                       acttccgttcagggtggtttcgcacccttgacatcgggtgttg                ttccgggcccctgtacgagtaattac
                                                                                                            

Query   TLND <---Intron---> VPVWSKLESGHLPSMQQLVQILDNEMKMNVHMNTRPHHHS
        |||| <   269bp    > |||||||||| |||||||||||||||||||||||||||||
Target  TLND                VPVWSKLESGQLPSMQQLVQILDNEMKMNVHMNTRPHHHS
        atag                gcgttacgtgccctacccgcacgagaaaagcaaaacccct
        cta                atctgcatacgatcctaattattaaatatatatacgcaaac
        aat                tgccgaagaatggtcgggtggcgccggggttcgcaaattca
                                                                    
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 220 ; UGA-SECIS: 658

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KV884716.1:subseq_1091911,100000_ Strand = - Positions = 44854 - 44780
 Found by:  Infernal (score=37.8) Covels (score=33.17)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -20.69

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .({(((((((--....{[[[(((((({((((................))))}))))))]]]}..--...)))))))}).
 target  UGAAGUGAUG--UUUAUGAAGGUCUGCGCUGAAGGCAGGAAGACUGCUAGCACAGACUGGAUGC--UCUCAUCACUCUU
                         ****           ^^                         ****