_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:1     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
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 Blastx evalue: 6e-19
 Query name: gi|942029055|ref|XP_005886875.2| PREDICTED: methionine-R-sulfoxide reductase B1 [Bos mutus]
 Query range: 1-115  (total 116)

 Target: /data/www-rg/seblastian_results/214267542/tempfiles/temptarget.fasta
 Chromosome: NW_018343886.1:subseq_1015579,62338_ Strand: -
 Positions:
 -Exon 1  32284        32338
 -Exon 2  30448        30596
 -Exon 3  29988        30128

 Redox box: no

Query   MSFCSFFGGEIFQNHFEPG <---Intron---> IYVCAKCGYELFSSRSKYAHSSPWPAFTETIHADSVAKRPEHNRPGAIK <---Intron---> 
        ||||||||||/|||||||| <   1687bp   > ||||||||||||||||||||||||||||||||||||||||||||||||| <   319bp    > 
Target  MSFCSFFGGEVFQNHFEPG                IYVCAKCGYELFSSRSKYAHSSPWPAFTETIHADSVAKRPEHNRPGAIK                
        atttattggggtcactgcg                atgtgatgtgcttactatgcttctcgtagaacggaggaccgcaccggaa                
        tctggttggattaaatac                gtatgcaggaattcggcaacacccgcctcactacagtcagcaaagcgcta                
        ggcccccgcgtcgcctgg                tccgtcgtctgccccccgcacgcaggcccgccctctgcgtagttgtacag                
                                                                                                            

Query   VSCGRCGNGLGHEFLNDGPKRGQSRFUIFSSSLKFIPKAEETSTSQG
        ||||||||||||||||||||||||||||||||||||||    |   |
Target  VSCGRCGNGLGHEFLNDGPKRGQSRFUIFSSSLKFIPKGALASWHLG
        gttgatgagcgcgtcaggcacgctcttataattatacaggcgttccg
        tcgggggagtgaattaagcaggacgtgttggctattcagctccgatg
        actcgtctggctgcgctccgcagcccatcccaggcctatgttcgcgc
                                  *                    
 Sequence until next stop: 
ACAGGCCTGTGTAAACTTTAG
 T  G  L  C  K  L  * 

 Distance CDS-SECIS: 1740 ; UGA-SECIS: 1800

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = NW_018343886.1:subseq_1015579,62338_ Strand = - Positions = 28247 - 28177
 Found by:  Infernal (score=34.55) Covels (score=27.04)
 Stem2 length = 10   Apical loop length = 14   Insertion in stem2 = 0, 0
 Free Energy = -20.94

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .({((((((---....{[[{(({((((((((.....-.........))))))))}))}]]}..--..-.))))))}).
 target  CCCGGUCAC---UCUAUGAUUCUCUCUGGUUAAACC-CUUGCAGGCAGCCAGAGUGGUGAUGA--CC-UGUGACCCGC
                         ****           ^^^                       ****