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

 Blastx evalue: 1e-19
 Query name: gi|831542775|ref|XP_012725247.1| PREDICTED: selenoprotein M-like [Fundulus heteroclitus]
 Query range: 1-139  (total 139)

 Target: /data/www-rg/seblastian_results/234762590/tempfiles/temptarget.fasta
 Chromosome: SSNR01003313.1 Strand: +
 Positions:
 -Exon 1  1138         1254
 -Exon 2  1570         1646
 -Exon 3  1752         1830
 -Exon 4  2180         2320

 Redox box: no

Query   MIYKMWAFLVFTFTLAAGTSESSNDTAAEERLVIARGKLM <---Intron---> APSVVGUGIKKMPELHHFLMERWALY <---Intron---> HN
         | |||  || || | || |// |/|||| / |||||||/ <   315bp    > ||||||| |||||||||||/|||||| <   105bp    > ||
Target  FILKMWTVLVLTFAL-AGASDTDNNTAAEIKPVIARGKLL                APSVVGUAIKKMPELHHFLLERWALY                HN
        tacaatagcgcatgc-gggtgagaaagggaacgagcgacc                gcagggtgaaaacgccctccgctgtt                ca
        tttatgcttttctct-cgccacaaacccatacttcggatt                ccgttggctaatcataatttaggcta                aa
        tcaaggccggcgtac-taaactcccagtatgacatataag                tctgcaacagagagcttcgggagtg                ccc
                                                                      *                                     

Query   LEYDSSEEKNPRLIFYNEKDEVVK <---Intron---> TVPVKNMKADEISSLLESLGFYKRSKKGEEVPEEFQNFPLHAPRDEL
        |||||||||||||||||/|||||/ <   349bp    > ||||| ||||||||||/||||||||/|||||||||||||||||||||
Target  LEYDSSEEKNPRLIFYNDKDEVVQ                TVPVKKMKADEISSLLDSLGFYKRSQKGEEVPEEFQNFPLHAPRDEL
        tgtgttggaacccattagaggggc                agcgaaaagggaaaccgtcgttaatcaggggcggtcatcccgcaggc
        taaaccaaaacgtttaaaaaatta                ctctaatacaatggttactgtaagcaagaatcaataatctaccgaat
        gatcaagggttcgacttcgtatag                gctggagggtgcccggcagtccggcgagagaaggcgtccgcccgcgg
                                                                                               
 Sequence until next stop: 
TGA
 * 

 Distance CDS-SECIS: 28 ; UGA-SECIS: 304

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = SSNR01003313.1 Strand = + Positions = 2349 - 2440
 Found by:  Infernal (score=24.77) Covels (score=22.27)
 Stem2 length = 10   Apical loop length = 20   Insertion in stem2 = 0, 0
 Free Energy = -30.9

         ..(((((((............(((((((((((((((....................))))))))))))))).............)))))))..
 model   uucggucaugcg-----UuaAUGAcGgccuggcccuAAAcC-----cuuuuuggggcgggccaggcCuGAUGuu----u-uuucaugaccggc
         (((((((((............([[{((((({(((((....................)))))})))))}]]).........-...)))))))))
 target  GCUGCAGCCUGGUUGCUGUAAUGACGAGUGAGGCCUAAAGGCCAAAACAUUAGGUCAGGCUCCACUCUGAGGACUCGCUG-GCUGGCUGCAGU
                              ****           ^^^                            ****