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

 Blastx evalue: 1e-22
 Query name: gi|315013579|ref|NP_001186661.1| selenoprotein S [Equus caballus]
 Query range: 1-190  (total 190)

 Target: /data/www-rg/seblastian_results/723078184/tempfiles/temptarget.fasta
 Chromosome: gi|398922816|gb|JH767761.1|:subseq_4189092,106695_ Strand: +
 Positions:
 -Exon 1  49226        49301
 -Exon 2  50001        50135
 -Exon 3  51917        52023
 -Exon 4  54609        54698
 -Exon 5  54799        54877
 -Exon 6  56652        56734

 Redox box: no

Query   MEPDEERLSARPAVEAEGLRFLHVTV <---Intron---> GSLLAAYGWYLVFSCILLYVLFQKLSSRLRALRQRRLDRAAAAVE <---Intron--
        || |||/||||||/| |||||||||| <   699bp    > ||||| ||||/|||||||||/|||||/||||||||/||||||||| <   1781bp  
Target  MEVDEEQLSARPALETEGLRFLHVTV                GSLLATYGWYIVFSCILLYVVFQKLSTRLRALRQRQLDRAAAAVE             
        agggggcctgccgcgaggcctccgag                gtccgatgttagtatacctggtcactaccagtacaccgcgggggg             
        tataaaatccgcctacagtgttatc                tgcttccaggatttggtttatttaatccgtgctgagatagcccct              
        ggccggggcgggtggcggaccgctg                gctggcctcgccccccctccgtcgggcccggcgggggacatgtcg              
                                                                                                            

Query   -> PDVVVKRQEALAAARLKMQEELNAQVEKHKEKLRQ <---Intron---> LEEEKRRRKIEMWDSMQEGKSYKRNARGPQ <---Intron---> 
         > ||/|||||||||||||||||||||||||||||||| <   2585bp   > ||||||||||||||||||||||||||  || <   100bp    > 
Target     PDIVVKRQEALAAARLKMQEELNAQVEKHKEKLRQ                LEEEKRRRKIEMWDSMQEGKSYKRNAGRPQ                
           cgaggaccggtgggctaacggcagcggacagacac                cgggaaacaagatgaacggaataaaggacc                
          acatttagaactcccgtataaatacataaaaaatga                taaaagggatatgagtaagagaagacggca                
          atttttagaataatttgagagaataatagtggaaag                taagagaggtaggccgaaaatcaataagtg                
                                                                                                            

Query   EEDSPGPSTSSVIPKRKSDRKPLRGGG <---Intron---> YNPLSGEGGGACSWRPGRRGPSSGGUG
        ||||||||||||||||||||||||||| <   1774bp   > |||||||||||||||||||||||||||
Target  EEDSPGPSTSSVIPKRKSDRKPLRGGG                YNPLSGEGGGACSWRPGRRGPSSGGUG
        gggacgctattgacacatgaactcggg                tacttggggggtttacgcagcttggtg
        aaagcgcccccttcagacagactggg                gaactcgagggcgcggcggggcccgggg
        aacttgtttcaccgaaatcagtggat                tcctgttaatacccgattcacgattaac
                                                                            * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 356 ; UGA-SECIS: 359

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = gi|398922816|gb|JH767761.1|:subseq_4189092,106695_ Strand = + Positions = 57091 - 57165
 Found by:  Infernal (score=22.69) Covels (score=41.01)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -5.93

         ..(((((((.......(((((((((((((((.................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...((({{(---....{[[{(({{(((((((.................)))))))}}))}]]}..--....)}})))...
 target  AGUUUGCGU---UGAAUGAUGUCUUCCUUGUAAAUGGUGAGCCCACCAGCGAGGAUUACUGAUGC--AGACAGUUGAUGG
                         ****           ^^^                         ****                 
