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

 Blastx evalue: 2e-19
 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/281941911/tempfiles/temptarget.fasta
 Chromosome: OMLM01020828.1:subseq_0,66886_ Strand: +
 Positions:
 -Exon 1  15774        15828
 -Exon 2  16485        16627
 -Exon 3  16776        16898

 Redox box: no

Query   MSFCQFFGGEIYKDHFKPG <---Intron---> VYVCSKCNHPLFSSRSKFAHSSPWPAFTETIREDSVTKMMETLTAYK <---Intron---> VL
        ||||||||||||||||||| <   656bp    > /||||||||||||||||||||||||||| |||||||||/|||||||| <   148bp    > ||
Target  MSFCQFFGGEIYKDHFKPG                MYVCSKCNHPLFSSRSKFAHSSPWPAFTHTIREDSVTKLMETLTAYK                VL
        atttcttgggatagctacg                atgttatacccttactatgcttctcgtacaaaggagaacagacagta                gc
        tctgattggataaaatac                gtatgcagaacttcggcatcacccgcctcactgaagtcattactccaa                tt
        gtctgttgtgccatttaa                cgcgccgtctcgcctgcgcccgtagggctcccagctccagggactatg                cg
                                                                                                            

Query   CGKCGNGLGHEFVNDGPEEGISRFUIFSHSLKFVPGKGK
        |||||/||||||/|/|||||/|||||||||||||| |||
Target  CGKCGSGLGHEFLNNGPEEGVSRFUIFSHSLKFVPSKGK
        tgatgagcgcgttaagcggggtcttatactcatgcaaga
        ggaggggtgaattaagcaagtcgtgttgactattcgaga
        tcgtctggctgtgttcagaacgttaacccgcgtcccatg
                                *              
 Sequence until next stop: 
ATAACCACATATATGTGTTTCATAACAATTTAA
 I  T  T  Y  M  C  F  I  T  I  * 

 Distance CDS-SECIS: 728 ; UGA-SECIS: 770

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = OMLM01020828.1:subseq_0,66886_ Strand = + Positions = 17627 - 17703
 Found by:  Infernal (score=25.81) Covels (score=16.25)
 Stem2 length = 10   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -18.11

         ..(((((((.......(((((((((((((((.................))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ..([(((((.--....([[{((((((((((...................))))))))))}]]).....-.-.)))))])..
 target  UUUGGGUUAC--UGGGUGACGUGGACAGGAGAAAAGCCUGAAAGUGACGUCCUGUCCACUGAAGAAUG-U-UUGACCAGUC
                         ****           ^^^                         ****