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

 Blastx evalue: 2e-23
 Query name: gi|239504580|ref|NP_001155120.1| selenoprotein M precursor [Sus scrofa] >gi|237930353|gb|ACR33808.1| selenoprotein M [Sus scrofa]
 Query range: 9-142  (total 142)

 Target: /data/www-rg/seblastian_results/138604057/tempfiles/temptarget.fasta
 Chromosome: gi|431920835|gb|KB030308.1|:subseq_4819670,250000_ Strand: -
 Positions:
 -Exon 1  12037        12132
 -Exon 2  10758        10793
 -Exon 3  10501        10535
 -Exon 4  10054        10132
 -Exon 5  9818         9973

 Redox box: YES

Query   PLLLLLAALAAATTTFRPDWNRLQGLARARVE <---Intron---> TCGGUQLNRLKE <---Intron---> VKAFVTQDIPLY <---Intron-
        ||||| |||||||||||||||||  ||| ||| <   1243bp   > |||||||||    <   222bp    > |||||||||||| <   368bp  
Target  PLLLLFAALAAATTTFRPDWNRLHRLARGRVE                TCGGUQLNRXXX                VKAFVTQDIPLY            
        ccccctggcgggaaatccgtacccccgcgcgg                atggtccacnnn                gagtgacgactt            
        ctttttcctcccccctgcagagtagtcgggta                cggggatagnnn                tacttcaatcta            
        cgggtcgaccctccccgccgctgccgcacggg                ctgaaggcnnnn                ggctccgccag             
                                                            *                                               

Query   --> HNLVMKHLPGADPELVLLGHRFEELE <---Intron---> RIPLSDMTREEINALVQELGFYRKAAPEDPVPPEYMRAPARPAEGAPDRADL
          > |||||||||||||||||||||/|||| <    80bp    > |||||/|||/|||||||||||||||||/|||||||/||||||||||||||||
Target      HNLVMKHLPGADPELVLLGHRYEELE                RIPLSEMTRKEINALVQELGFYRKAAPDDPVPPEYLRAPARPAEGAPDRADL
            cacgaacccgggcgcgccgcctggtg                caccagaacagaagcgcgcgttcaggcggcgccgtccgcgacggggcgcggc
            aatttaatcgcacattttgagaaata                gtctgatcgaatacttaatgtagacccaactccaatgcccgccagccagcat
           cctgagatcggccagtaggccccagag                acaccagccggccaggggccctcgggccctgccacgggctgccgctgcctcg
                                                                                                          
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 34 ; UGA-SECIS: 325

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|431920835|gb|KB030308.1|:subseq_4819670,250000_ Strand = - Positions = 9783 - 9711
 Found by:  Infernal (score=17.94) Covels (score=17.28)
 Stem2 length = 9   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -25.67

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((---....{[[{(({(((((((..................)))))))}))}]]}..--..-.)))))))..
 target  CCUGGGGAC---AGAAUGAAGCGCUCAGCGUCCCGGGAACACCUCCCUCGCUGAGGGUCGACGC--CC-CGUCCCCAAG
                         ****           ^^                         ****