_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:1     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
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 Blastx evalue: 4e-24
 Query name: gi|908479522|ref|XP_003438768.2| PREDICTED: methionine-R-sulfoxide reductase B1-A-like [Oreochromis niloticus]
 Query range: 1-106  (total 110)

 Target: /data/www-rg/seblastian_results/715747493/tempfiles/temptarget.fasta
 Chromosome: KV884859.1:subseq_721558,100000_ Strand: +
 Positions:
 -Exon 1  49332        49386
 -Exon 2  50001        50143
 -Exon 3  50307        50426

 Redox box: no

Query   MSFCQFFGGEIYKDHFKPG <---Intron---> VYVCSKCNHPLFSSRSKFAHSSPWPAFTETIREDSVTKMMETLTAYK <---Intron---> VL
        |||||||  |/|/|/| || <   614bp    > /|||| ||||||||||||||||||||| /||||||||| |||||||| <   163bp    > ||
Target  MSFCQFFDRELYRDNFTPG                MYVCSMCNHPLFSSRSKFAHSSPWPAFADTIREDSVTKQMETLTAYK                VL
        atttcttgcgctcgatacg                atgttatacccttactatgcttctcgtggaaaggagaacagacagta                gt
        tctgattagatagaatcc                gtatgctgaacttcggcatcacccgcctcactgaagtcaatactccaa                tt
        gactgttctgccgttcaa                tgtgccgtctcgcctccgttcgccggtttcccagctccagggtctccg                cg
                                                                                                            

Query   CGKCGNGLGHEFVNDGPEEGISRFUIFSHSLKFVPGKG
        ||||||||||||/||||/||/||||||||||||/| ||
Target  CGKCGNGLGHEFLNDGPKEGVSRFUIFSHSLKFIPSKG
        tgatgagcgcgttaggcagggtcttatactcatacaag
        ggaggagtgaattaagcaagtcgtgttgactattcgag
        tcgtccggctgtgttaaggagattaacccgggccccat
                                *             
 Sequence until next stop: 
ATTATGAGTGAAACATTCTAG
 I  M  S  E  T  F  * 

 Distance CDS-SECIS: 1017 ; UGA-SECIS: 1056

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KV884859.1:subseq_721558,100000_ Strand = + Positions = 51444 - 51517
 Found by:  Infernal (score=19.0) Covels (score=17.33)
 Stem2 length = 9   Apical loop length = 20   Insertion in stem2 = 0, 0
 Free Energy = -22.45

         ..(((((((.......(((((((((((((((..................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC---cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         (([((((((---....([[{((((({((((....................))))})))))}]])..--.--.))))))]))
 target  ACGGGUCAG---CGGGUGAUGUGGAGGGGAGAAAGGCCUGAAGAGGGACAUCCUGUCCACUGAAGA--A--UCUGACCAGU
                         ****           ^^^                          ****