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

 Blastx evalue: 3e-10
 Query name: gi|992225227|ref|XP_007260428.2| PREDICTED: selenoprotein W [Astyanax mexicanus]
 Query range: 1-86  (total 86)

 Target: /data/www-rg/seblastian_results/563837871/tempfiles/temptarget.fasta
 Chromosome: CM008302.1:subseq_11542115,100074_ Strand: -
 Positions:
 -Exon 1  53249        53277
 -Exon 2  52010        52034
 -Exon 3  51858        51911
 -Exon 4  50000        50074
 -Exon 5  49579        49653

 Redox box: YES

Query   MGVKIHIIYC <---Intron---> GGUGYRPK <---Intron---> YTKLKTLLEDEFPGDLEI <---Intron---> SGESTPRTSGWFEVEV
        |||||||||| <   1214bp   > |||||||| <    98bp    > |||||||||||||||||| <   1783bp   > ||||||||||||||||
Target  MGVKIHIIYC                GGUGYRPK                YTKLKTLLEDEFPGDLEI                SGESTPRTSGWFEVEV
        aggaacaatt                ggtgtaca                taacaatcgggtcggcga                tggaacaatgttgggg
        tgtatattag                ggggagca                acatacttaaatcgatat                cgagccgccggtatat
        ggtaacaac                ttaagcacg                ccacgggtgtatacctgt                ttgcccaagggtgagg
                                    *                                                                       

Query   NGKLVHSKK <---Intron---> NGDGFVDSDQKMAKIVSAIEKSIGK
        ||||||||| <   346bp    > |||||||||||||||||||||||||
Target  NGKLVHSKK                NGDGFVDSDQKMAKIVSAIEKSIGK
        agacgctaa                agggtggtgcaagaagagagataga
        agattacaa                agagttacaaatcattgctaactga
        tcgggccgg                tgtctgcttgggcgtgttcggctca
                                                          
 Sequence until next stop: 
TGA
 * 

 Distance CDS-SECIS: 1139 ; UGA-SECIS: 1358

------- SECIS element -- id:1 -- grade:B ----
 Chromosome = CM008302.1:subseq_11542115,100074_ Strand = - Positions = 48439 - 48362
 Found by:  Infernal (score=17.03) Covels (score=25.55)
 Stem2 length = 8   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -12.74

         ..(((((((.......(((((((((((((((...............)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ..((({(((((.....{[[{(((({({{(((.....-.........)))}})}))))}]]}......-.)))))})))..
 target  UCUGGCAGUGCAACAAUGAUGGUGACUUCCGAAGUG-UCUUUGACACGGUUGCUACUUGAUGCUUAC-CGCAUUUCUAAG
                         ****           ^^                        ****