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

 Blastx evalue: 1e-23
 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/766403479/tempfiles/temptarget.fasta
 Chromosome: CM007954.1:subseq_20289667,100770_ Strand: -
 Positions:
 -Exon 1  50716        50770
 -Exon 2  50277        50419
 -Exon 3  49994        50113

 Redox box: no

Query   MSFCQFFGGEIYKDHFKPG <---Intron---> VYVCSKCNHPLFSSRSKFAHSSPWPAFTETIREDSVTKMMETLTAYK <---Intron---> VL
        |||| || ||/|||||||| <   296bp    > /||||/||/||||||||| ||||||||||||/|||||||||/|||/| <   163bp    > ||
Target  MSFCSFFDGEVYKDHFKPG                MYVCSQCNNPLFSSRSKFLHSSPWPAFTETIKEDSVTKMMESLTAFK                VL
        attttttggggtagctacg                atgttctaaccttaatatccttctcgtagaaaggagaaaagtcagta                gc
        tctgcttagataaaatac                gtatgcagaacttcggcattacccgcctcactaaagtcattactccta                tt
        gttcatttcgctactcaa                tgtgttgcccggcccgtgcccccggtcctgccagctccggggacaccg                gt
                                                                                                            

Query   CGKCGNGLGHEFVNDGPEEGISRFUIFSHSLKFVPGKG
        ||||||||||||||||||||||||||||/|||||| ||
Target  CGKCGNGLGHEFVNDGPEEGISRFUIFSNSLKFVPNKG
        tgatgagcgcgtgaggcgggatcttataatcatgcaag
        ggaggagtgaattaagcaagtcgtgttgactattcaag
        tggttcaactgtccctggatcaacaacccgcgtcatat
                                *             
 Sequence until next stop: 
AACGTGCCGAAATACCAATCAGAAAAAAAGAACTGTTTGGTTTATGTGTAG
 N  V  P  K  Y  Q  S  E  K  K  N  C  L  V  Y  V  * 

 Distance CDS-SECIS: 271 ; UGA-SECIS: 310

------- SECIS element -- id:1 -- grade:B ----
 Chromosome = CM007954.1:subseq_20289667,100770_ Strand = - Positions = 49722 - 49646
 Found by:  Infernal (score=19.08) Covels (score=14.97)
 Stem2 length = 9   Apical loop length = 21   Insertion in stem2 = 0, 0
 Free Energy = -19.1

         ..(((((((.......(((((((((((((((.................))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ..(((((((.--....{[[{((([(((((.....................)))))])))}]]}.....-.-.)))))))..
 target  GACUGGUCAG--UAUGUGACGUGGACAGGAACAAGGCCCAGGAGGGACACCCUGUACACUGAUGACUC-U-AUGACCAGCC
                         ****         ^^                            ****