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

 Blastx evalue: 2e-24
 Query name: gi|301897553|ref|NP_001180433.1| selenoprotein Ja [Oncorhynchus mykiss]
 Query range: 1-344  (total 344)

 Target: /data/www-rg/seblastian_results/611407804/tempfiles/temptarget.fasta
 Chromosome: CM007945.1:subseq_18631130,107313_ Strand: -
 Positions:
 -Exon 1  58373        58442
 -Exon 2  57573        57752
 -Exon 3  57324        57422
 -Exon 4  55763        55855
 -Exon 5  55334        55490
 -Exon 6  53724        53839
 -Exon 7  52794        52871
 -Exon 8  51864        52003
 -Exon 9  49899        49997

 Redox box: no

Query   MMASTVAERAMGAIIGAAVADAAA <---Intron---> QPMHWIYNPERLKEVLSDLEPCPEFRPQSANPFYRRETGEQTCYGDQVYVLLESLSQCGD
         ||||||||||||||||||||||| <   620bp    > ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Target  QMASTVAERAMGAIIGAAVADAAA                QPMHWIYNPERLKEVLSDLEPCPEFRPQSANPFYRRETGEQTCYGDQAYVLLESLSQCGD
        cagtagggagaggaaggggggggg                ccactatacgccaggctgcgctcgtccctgacttcagaggcattggcgtgccgtcactgg
        atccctcagctgcttgcctcacc                cactagtaacagtaattcatacgcatgcaccactaggacgaacgagaacatttactgagg 
        ggtatgagacggactaatgacaa                cgcgtgtccagagggtgatgagtagcctgttcgcccagcagggccacgccagagactata 
                                                                                                            

Query    <---Intron---> VNVEDLTKRIYKFFGPDTVYDLPLNNPYRQKNG <---Intron---> PKAVLPIGGPWRNASLKAFMRNVDAGNEKTG <--
         <   150bp    > ||||||||||||||||||||||||||||||||| <   1468bp   > ||||||| ||||||||||||||||||||||| <  
Target                  VNVEDLTKRIYKFFGPDTVYDLPLNNPYRQKNG                PKAVLPIDGPWRNASLKAFMRNVDAGNEKTG    
                        gagggtaacatattgcgagtgcccaactacaag                caggccaggctaagacagtaaaggggagaag    
                       atataatcagtaattgcactaatctaacagaaa                gcacttctagcggacgtacttgatacgaaac     
                       tgcggcgcacccgctcactgttttctcacaagc                ttatcgcttctgacaccaccggcgtaacaga     
                                                                                                            

Query   -Intron---> CDVDCQMDGVTKMAPVVAMFAGMPEMLEKVETAIRVTQNNDMCVAMTLAAAR <---Intron---> FLEHFILNGSDPNALDSVLA
         272bp    > |||||||||||||||||||||||||||||||||||||||||||||||||||| <   1494bp   > ||||||||||||||||||||
Target              CDVDCQMDGVTKMAPVVAMFAGMPEMLEKVETAIRVTQNNDMCVAMTLAAAR                FLEHFILNGSDPNALDSVLA
                    tgggtcagggaaagcgggatggacgatgaggagacgacaagatggaacggga                tcgctacagtgcagcgtgtg
                   ggatagatagtcatccttcttcgtcattaatacctgtcaaaatgtctctcccg                ttaatttagcacactacttc
                   attgctggcgccggtctgggttgggggggggggcttacgcctgtgcgagtaa                gcggtccgtttccttgcaggc
                                                                                                            

Query   QLNDPNRNNPQDLDRAVIA <---Intron---> QICQVKDNLSKHSPELIPAVFTNTUA <---Intron---> LPGAFQGALHGVLTMSQLEEAVR
        ||||||||||||||||||| <   852bp    > |||||||||||||||||||||||||| <   790bp    > |||||||||||||||||||||||
Target  QLNDPNRNNPQDLDRAVIA                QICQVKDNLSKHSPELIPAVFTNTUA                LPGAFQGALHGVLTMSQLEEAVR
        ccagcaaaaccgcgaggag                catcgagattactcgcacggtaaatg                tcggtcggccggcaaaccgggga
        ataacagaacaatagctt                catgataaatcaaccattccttcacg                ctcgctagctagttctgataactg
        gcccacacctgcgcgttt                aactgggccacgtcaggattgctcaa                cgatacgaagcgcgagcggggacg
                                                                   *                                        

Query   GTMRRGGCTASRASFIGACFGAQ <---Intron---> TGLQGIPESWKNRTLKYPVLLGLAKKVVGSQQA
        ||||||||||||||||||||||| <   1866bp   > |||||||||||||||||||||||||||||||||
Target  GTMRRGGCTASRASFIGACFGAQ                TGLQGIPESWKNRTLKYPVLLGLAKKVVGSQQA
        gaaccggtagaagttaggttggc                agccgacgttaaaacatcgccgcgaagggtccg
        gctgggggccggccttgcgtgca                cgtagtcacgaagctaactttgtcaattgcaac
        acgccgaccctgcacagcttaag                attgacagtggcgccattgggagtgatacagac
                                                                                
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 170 ; UGA-SECIS: 410

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM007945.1:subseq_18631130,107313_ Strand = - Positions = 49728 - 49656
 Found by:  Infernal (score=31.15) Covels (score=24.01)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -14.69

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         (((({({(((--(...([[(((((((((((......-..........)))))))))))]])..--..))))})}))))
 target  GACAAAACAG--UUUAUGAAAGUUACAUUCUAAAGU-AACAUUUGACGGAUGUAACUUGAACC--UUGUUGCUCUGUC
                         ****           ^^^                       ****