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

 Blastx evalue: 1e-18
 Query name: gi|315113844|ref|NP_001186679.1| selenoprotein S [Taeniopygia guttata]
 Query range: 1-189  (total 189)

 Target: /data/www-rg/seblastian_results/711017354/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: -
 Positions:
 -Exon 1  52924        53005
 -Exon 2  52645        52779
 -Exon 3  51088        51194
 -Exon 4  50167        50256
 -Exon 5  50002        50077
 -Exon 6  47969        48051

 Redox box: no

Query   MDLGDGGPAAGPG--LGRGGLEALQHTV <---Intron---> GSVLSGYGWYVLLAAVAVYLLVQKVSRSLAARPGGRPGAAEAAEE <---Intron
        ||||||| |||||  ||||||||||||| <   144bp    > ||||||||||/|||||||||||||||| ||||||||||||||||| <   1450bp
Target  MDLGDGGAAAGPGPALGRGGLEALQHTV                GSVLSGYGWYLLLAAVAVYLLVQKVSRGLAARPGGRPGAAEAAEE           
        agcggggggggcgcgcgcggcggcccag                gtgctgtgttcccgggggtccgcagtcgcggccggccgggggggg           
        tatgaggcccgcgcctggggtactaac                tgcttcgaggatttcctctatttaatcggtccgcgggcgccacca            
        gtcgcctcggccggggcgcggggggcg                gcgggcctcgcgggccccgcgcggggccggggggccgcagggggg            
                                                                                                            

Query   ---> PDVVVRRQEALAAARLRMQEELNAQAEKYKEKQRQ <---Intron---> LEEERRRQKIVMWESMQEGKSYKGNLKLNQ <---Intron---
           > ||||||||||||||||||||||||||||||||||| <   831bp    > |||||||||| ||||||||||||||||||| <    89bp    
Target       PDVVVRRQEALAAARLRMQEELNAQAEKYKEKQRQ                LEEERRRQKIAMWESMQEGKSYKGNLKLNQ              
             cggggaacggtgggccaacggtagcggatagacac                cgggccccaagatgaacggaatagacacac              
            acatttggaactcccgtgtaaatacacaaaaaaaga                taaagggaatctgagtaagagaagatataa              
            gttggaaggatgaatccggagagtaaaaacaagaag                gggggggggcggggcggaagccaacgagtg              
                                                                                                            

Query   > EVESAASSASAVPKSKPNKKPLRGGG <---Intron---> YNPLSGEGGGTCSWRPGRRGPSAGGUG
        > /   / /||||||||||||||||||| <   1950bp   > |||||||||||||||||||||||||||
Target    QEVESGASASAVPKSKPNKKPLRGGG                YNPLSGEGGGTCSWRPGRRGPSAGGUG
          cgggtggtgtggcatacaaactaggg                tacctgggggatttacgccgctgggtg
          aatacgccccctcacacaaactggg                gaactcgagggcgcggcggggcccgggg
          aaaattctcaacgagaacagcgaat                ctccgtaaaaggccggccggcgcataac
                                                                             * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 552 ; UGA-SECIS: 555

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = - Positions = 47416 - 47331
 Found by:  Infernal (score=23.89) Covels (score=39.27)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -8.73

         ..(((((((................(((((((((((((((.................)))))))))))))))........)))))))..
 model   uucggucaugcg---------UuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(({((((................{[[{(({{(((((((.................)))))))}}))}]]}..--..-.))))}))..
 target  GGUCUCUGUGACAAGCCAGCUUGAAUGAUGUNUUCCUUAUAAAUGGUAAACAAACCAGUGAGGAUUACUGAUGC--UA-GACAGCGGAC
                                  ****           ^^^                         ****