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

 Blastx evalue: 4e-16
 Query name: gi|1041109462|ref|XP_017278043.1| PREDICTED: selenoprotein T1a-like [Kryptolebias marmoratus]
 Query range: 1-194  (total 194)

 Target: /data/www-rg/seblastian_results/642225076/tempfiles/temptarget.fasta
 Chromosome: SSNR01000216.1:subseq_957020,103341_ Strand: -
 Positions:
 -Exon 1  55246        55379
 -Exon 2  53226        53336
 -Exon 3  51497        51623
 -Exon 4  50195        50282
 -Exon 5  49878        49999

 Redox box: YES

Query   MNRLRFSLLALGLFSLCCATTGDSSGVKKMKMQFATGPLLKFQIC <---Intron---> ISUGYKRVFEEYTQALYQRYPDIRIEGENYLPIPVYR <
        |  |||||||||||||||||||||||||||||||||||||||||| <   1909bp   > ||||||||||||||||||||||||||||||||/|/|| <
Target  MKWLRFSLLALGLFSLCCATTGDSSGVKKMKMQFATGPLLKFQIC                ISUGYKRVFEEYTQALYQRYPDIRIEGENYLPMPIYR  
        aattcttccgtgcttcttgaaggaaggaaaaactgagcccatcat                attgtacgtggtacgttcctcgacagggatccacatc  
        tagtgtcttctgttctggcccgagggtaatatatccgcttatatg                tcggaagttaaacactaagacatgtagaaatctctag  
        ggggttgcttggtcttcccgttcttcgaggggattgttttgtat                ctcagcgggtggcggcgcggcaccctaggtcttgcct   
                                                                       *                                    

Query   ---Intron---> HIASFLSMFKLLVIGLIIIGRDPFAFFGMQSPGIWQWGQENK <---Intron---> IYACMMVFFFSNMIENQLMSTGAFEITL
           1602bp   > ||||||||||||||||||||/|||||||||/||||/||| || <   1214bp   > ||||||||||||||||||||||||||||
Target                HIASFLSMFKLLVIGLIIIGKDPFAFFGMQAPGIWEWGQGNK                IYACMMVFFFSNMIENQLMSTGAFEITL
                      cagttctataccgagcaaagagctgttgacgcgatgtgcgaa                atgtaagtttaaaagactataggtgaat
                      atccttcttattttgttttgaactcttgtaccgtgaggagaa                tacgttttttgattaaattccgctatct
                     actcccgtgcagggtggttccgcatccttgacagcgggcgatg                atccgggcccctgtacgagaaaatacga
                                                                                                            

Query   ND <---Intron---> VPVWSKLESGHLPSMQQLVQILDNEMKMNVHMNTRPHPHS
        || <   195bp    > ||||||||||||||||||||||||||||||||||||||||
Target  ND                VPVWSKLESGHLPSMQQLVQILDNEMKMNVHMNTRPHPHS
        ag                gcgttacgtgccctacccgcacgagaaaagcaaaacccct
        a                atctgcatacgatcctaattattaaatatatatacgcacac
        t                caaggaagggtcgtcgagtgacctcggggctcgcaaacccc
                                                                  
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 158 ; UGA-SECIS: 596

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = SSNR01000216.1:subseq_957020,103341_ Strand = - Positions = 49719 - 49645
 Found by:  Infernal (score=34.37) Covels (score=29.96)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -23.29

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .({(((((((--....{[[[{((((((((((................))))))))))}]]]}..--...)))))))}).
 target  UGAAGUGAUG--UUUAUGAACGUCUGCGCUGAAAGCGGGAAGACUGCUAGCGCAGACUGGAUGC--CCCCAUCGCUCUU
                         ****           ^^^                        ****