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

 Blastx evalue: 4e-22
 Query name: gi|929279812|ref|XP_014016768.1| PREDICTED: selenoprotein M-like [Salmo salar]
 Query range: 1-167  (total 167)

 Target: /data/www-rg/seblastian_results/369198770/tempfiles/temptarget.fasta
 Chromosome: CM007945.1:subseq_55952321,100497_ Strand: -
 Positions:
 -Exon 1  53073        53204
 -Exon 2  51699        51734
 -Exon 3  51515        51549
 -Exon 4  50420        50498
 -Exon 5  49928        50140

 Redox box: YES

Query   MNLLNVLQSEEIMWFFIFVSFLNCVSAYDVDLKKLDGLAKAKVE <---Intron---> SCGGUQLNRLRE <---Intron---> VKAFVTQDIPLY
        ||| |||||||||||| ||| ||||||||||||||||||||||| <   1338bp   > |||||||||||| <   149bp    > ||||||||||||
Target  MNLPNVLQSEEIMWFFFFVSLLNCVSAYDVDLKKLDGLAKAKVE                SCGGUQLNRLRE                VKAFVTQDIPLY
        aaccagcctggaatttttgaccatgtgtgggcaacggcgagagg                ttggtccaacag                gagtgacgacct
        tatcattacaattgtttttgttagtccaatataatagtcacata                cggggatagtga                tacttcaatcta
        gtcccggaagatggcctcccctctggcttatggagttcaagggg                tctaaggcggag                cactgcgcttt 
                                                                        *                                   

Query    <---Intron---> HNLVMKHIPGADPELVLLNHYYEELD <---Intron---> RIALSDMTRSEINELLEKLGFYKKAQPEDQVPEEFRFSPAKD
         <   1016bp   > |||||||||||||||||||||||||| <   279bp    > |||||||||||||||||||||||||| |||||||||||||||
Target                  HNLVMKHIPGADPELVLLNHYYEELD                RIALSDMTRSEINELLEKLGFYKKAQAEDQVPEEFRFSPAKD
                        cacgaacacgggcgcgccacttggcg                cagctgaactgaagccgatgttaagcgggcgcggtcttcgag
                        aatttaatcgcacattttaaaaaata                gtctcatcgcataattaatgtaaacacaaatcaatgtcccaa
                       ctcgaggcctgtccgtcccccccaggc                gtcgtcgcctgccgaggggcccggtgtgcgcaggccccccgc
                                                                                                            

Query   SPFKATPSSSSSAPAGNASSDSDAEAKHSDL
        |||||||  |||||| |||||||||||||||
Target  SPFKATP--SSSAPADNASSDSDAEAKHSDL
        actagac--tttgcggagttgtggggactgc
        gctaccc--ccccccaacccacacacaacat
        cccaacc--ctaccacctcattcagcgctcg
                                       
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 314 ; UGA-SECIS: 662

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007945.1:subseq_55952321,100497_ Strand = - Positions = 49613 - 49541
 Found by:  Infernal (score=25.81) Covels (score=25.37)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -19.64

         ..(((((((.......((((((((((.(((((...............))))).))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcCcuuuuuggggcgggc-caggcCuGAUGuuuuuucaugaccggc
         (((({(([((--....{[[{((((({(((((......---........)))))})))))}]]}..--...))]))}))))
 target  GCUGUGGAAC--UGAAUGACGCCCCUGGCUGUAAAAU---CUCCUGAUUGGCUUGGGGCCGAUGC--AACGUGUCCUGGU
                         ****            ^^^                        ****