_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       knownSP        |  secis_index:1     SeB_exonerate category:ALI_U |*|_|*|_|*|_|*|_|*|_|*|_|*|_|*|_
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 Blastx evalue: 2e-40
 Query name: gi|908479522|ref|XP_003438768.2| PREDICTED: methionine-R-sulfoxide reductase B1-A-like [Oreochromis niloticus]
 Query range: 1-107  (total 110)

 Target: /data/www-rg/seblastian_results/701226352/tempfiles/temptarget.fasta
 Chromosome: JACSYO010001932.1:subseq_1536927,100000_ Strand: +
 Positions:
 -Exon 1  50000        50054
 -Exon 2  50769        50911
 -Exon 3  51022        51144

 Redox box: no

Query   MSFCQFFGGEIYKDHFKPG <---Intron---> VYVCSKCNHPLFSSRSKFAHSSPWPAFTETIREDSVTKMMETLTAYK <---Intron---> VL
        ||||/| |||/|||||||| <   714bp    > /||||/||||||||||||||||||||||/||||||||||||/|||/| <   110bp    > ||
Target  MSFCRFVGGEVYKDHFKPG                MYVCSQCNHPLFSSRSKFAHSSPWPAFTDTIREDSVTKMMESLTAFK                VL
        atttctgggggtagctacg                atgttctacccttactatgcttctcgtagaaaggagaaaagacagta                gc
        tctggttggataaaatac                gtatgcagaacttcggcatcacccgcctcactgaagtcattagtccta                tt
        gcctgttctgccattcaa                tgtgccgtccagcctgcgcccgtcggccccccagctctggggtctccg                tg
                                                                                                            

Query   CGKCGNGLGHEFVNDGPEEGISRFUIFSHSLKFVPGKGK
        ||||||||||||||||||/|/|||||||||||||| |||
Target  CGKCGNGLGHEFVNDGPEDGVSRFUIFSHSLKFVPNKGK
        tgatgagcgcgtgaggcggggtcttatactcatgcaaga
        ggaggagtgaattaagcaagtcgtgttgactattcaaga
        tagtccgcctgtatccggcacgctaactcgcgtcacata
                                *              
 Sequence until next stop: 
ATGACCACAGACGTGAGTGAGACATTGGCATGTGTGCAAGGCCAACGGTTTTAA
 M  T  T  D  V  S  E  T  L  A  C  V  Q  G  Q  R  F  * 

 Distance CDS-SECIS: 975 ; UGA-SECIS: 1017

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JACSYO010001932.1:subseq_1536927,100000_ Strand = + Positions = 52120 - 52194
 Found by:  Infernal (score=27.54) Covels (score=21.42)
 Stem2 length = 10   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -20.51

         ..(((((((.......(((((((((((((((.................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         .([((((((---....([[{((((((((((...................))))))))))}]])..--....))))))]).
 target  UCGGGUCAG---UGGGUGACGUGGACGGGGAAAAGGCCUGAGAGGGACGUCCUGUCCACUGAAGA--AUCUUUGACCAGC
                         ****          ^^^                          ****