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

 Blastx evalue: 5e-20
 Query name: gi|929095373|ref|XP_014058532.1| PREDICTED: methionine-R-sulfoxide reductase B1-A-like [Salmo salar]
 Query range: 1-110  (total 110)

 Target: /data/www-rg/seblastian_results/409899979/tempfiles/temptarget.fasta
 Chromosome: MSJN01022804.1:subseq_1,59999_ Strand: +
 Positions:
 -Exon 1  27256        27310
 -Exon 2  29163        29305
 -Exon 3  30866        30980
 -Exon 4  31168        31184

 Redox box: no

Query   MSFCSFFGGEVFKDHFKTG <---Intron---> LYVCAQCGHQLFSSRSKYEHSSPWPAFTETVLQDSVSKHEERPGAFK <---Intron---> VR
        ||||||||||||||||||| <   1852bp   > ||/|||||||||||||||||||||||||||/|||||||||||||||| <   1560bp   > ||
Target  MSFCSFFGGEVFKDHFKTG                LYMCAQCGHQLFSSRSKYEHSSPWPAFTETILQDSVSKHEERPGAFK                VR
        attttttggggtagctaag                ttatgctgcccttaatatgcttctcgtagaaccgagtacggacggta                gc
        tctgcttggattaaatac                gtatgcaggaattcggcaaaacccgcctcacttaagtcaaaagcgcta                tg
        gattcccttgctacctat                ggtgtcgtacggctcatgtgtcccgtcctgcccgctgcgtggatgacg                ca
                                                                                                            

Query   CGKCGNGLGHEFVGDGPKKGLSRFUIFSSSLKFVPKD <---Intron---> KVDGQ
        ||||||||||||||||||||||||||||||||||||| <   187bp    > |||||
Target  CGKCGNGLGHEFVGDGPKKGLSRFUIFSSSLKFVPKD                KVDGQ
        tgatgagcgcgtggggcaagctcttataatcatgcag                agggc
        ggaggagtgaattgagcaagtcgtgttggctattca                aataga
        tggtacagttgtgacgagaacatcaacccaggccta                tgatag
                                *                                 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 80 ; UGA-SECIS: 131

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = MSJN01022804.1:subseq_1,59999_ Strand = + Positions = 31265 - 31341
 Found by:  Infernal (score=31.54) Covels (score=28.08)
 Stem2 length = 10   Apical loop length = 19   Insertion in stem2 = 1, 0
 Free Energy = -20.31

         ..(((((((.......((((((((((((.(((.................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggc-ccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...((((((.--....{[[(((((((((.((...................)))))))))))]]}..--....))))))...
 target  UGCAGGACAG--UGGAUGAAGUGUCCUGGGAUAAAGCCCACUUUGGGACCUCCAGGACACUGAUGG--UCAAUGUCUUCGC
                         ****            ^^^                         ****