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

 Blastx evalue: 5e-08
 Query name: gi|928035970|ref|XP_013866582.1| PREDICTED: selenoprotein M-like [Austrofundulus limnaeus]
 Query range: 1-134  (total 134)

 Target: /data/www-rg/seblastian_results/956995644/tempfiles/temptarget.fasta
 Chromosome: KV884725.1:subseq_1272495,100000_ Strand: -
 Positions:
 -Exon 1  51532        51639
 -Exon 2  51121        51197
 -Exon 3  50768        50846
 -Exon 4  49878        50018

 Redox box: no

Query   MWALLVLTVALAAGASETND-TETEERPVIARGKLL <---Intron---> APSVVGUGIKKMPELHHFLMERWALY <---Intron---> HNLVYD
        ||  ||| /|||  |||||/ |  |   |||||||| <   334bp    > |||||||||||||||| ||||||||| <   274bp    > ||| ||
Target  MWIFLVLALALAVRASETNNATAAEGTLVIARGKLL                APSVVGUGIKKMPELHQFLMERWALY                HNLEYD
        atattgcgcgcggagtgaaagaggggacgagagacc                gcagggtgaaaacgccctcagctgtt                cacgtg
        tgtttttctctctgccacaaccccagctttcggatt                ccgttgggtaatcataatttaggcta                aataaa
        ggccggctcacttggaaacccattaagttacatagg                tctgcgacagagtgctgtcggggtg                cccgatt
                                                                  *                                         

Query   SSEEKDPRLIFYNEKDEVVK <---Intron---> TVPVKKMKADEISSLLDSLGFYKRSQKGEEVPEEFQNFPLHAPRDEL
        |||/|/|||||||||||||| <   749bp    > ||||||||||||||||||||||||||||||||||||/||||||||||
Target  SSEQKNPRLIFYNEKDEVVK                TVPVKKMKADEISSLLDSLGFYKRSQKGEEVPEEFQHFPLHAPRDEL
        ttgcaacccattagagggga                agcgaaaagggaaactgtcgttaatcaggggcggtcctcccgcaggc
        ccaaaacgtttaaaaaatta                ctctaatacaatggttactgtaagcaagaatcaataatctaccgaat
        aggggtctgacttagcgtag                ttcggaggacgcccgacactccggcaagaggaggcgtccgtccgtgg
                                                                                           
 Sequence until next stop: 
TGA
 * 

 Distance CDS-SECIS: 33 ; UGA-SECIS: 309

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KV884725.1:subseq_1272495,100000_ Strand = - Positions = 49844 - 49762
 Found by:  Infernal (score=26.13) Covels (score=19.26)
 Stem2 length = 11   Apical loop length = 20   Insertion in stem2 = 0, 0
 Free Energy = -24.57

         ..(((((((.......((((((((((.(((((..................))))).))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccug-gcccuAAAcC---cuuuuuggggcgggc-caggcCuGAUGuu-u-uuucaugaccggc
         ..((((((((......([[{(((((([((((....................))))]))))))}]])......-.-))))))))..
 target  ACCCUGGUCACAUUAAUGAUGAGUGGGGCCUCAAGGCCAAAACGAUAAGCCAGGCACCAUUCUGAGAACUUG-C-UGGCCAGGUG
                         ****            ^^                            ****