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

 Blastx evalue: 1e-19
 Query name: gi|315113844|ref|NP_001186679.1| selenoprotein S [Taeniopygia guttata]
 Query range: 4-189  (total 189)

 Target: /data/www-rg/seblastian_results/447317255/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: +
 Positions:
 -Exon 1  47313        47379
 -Exon 2  47505        47639
 -Exon 3  49038        49144
 -Exon 4  49973        50062
 -Exon 5  50153        50228
 -Exon 6  52179        52261

 Redox box: no

Query   GDGGPAAGPGLGRGGLEALQHTV <---Intron---> GSVLSGYGWYVLLAAVAVYLLVQKVSRSLAARPGGRPGAAEAAEE <---Intron---> 
        | |    || ||||||||||||| <   125bp    > ||||| ||||||||||||||||||||||||||| ||||||||||| <   1398bp   > 
Target  GAGRAGPGPALGRGGLEALQHTV                GSVLSSYGWYVLLAAVAVYLLVQKVSRSLAARPSGRPGAAEAAEE                
        gggcggcgcgcgcggcggcccag                gtgctatgttgccgggggtccgcagtcacggccagccgggggggg                
        gcggcgcgcctggggtactaac                tgcttcgaggatttcctctatttaatcggtccgcgggcgccacca                a
        agggcgcggggcgcggggggcg                gcgggccccgcgggccccgcccggggcccgggggccgcagggggg                g
                                                                                                            

Query   PDVVVRRQEALAAARLRMQEELNAQAEKYKEKQRQ <---Intron---> LEEERRRQKIVMWESMQEGKSYKGNLKLNQ <---Intron---> EVE
        |||||||||||||||||||||||||||||||||/| <   828bp    > |||||||||| ||||||||||||||||||| <    90bp    > /  
Target  PDVVVRRQEALAAARLRMQEELNAQAEKYKEKQKQ                LEEERRRQKIAMWESMQEGKSYKGNLKLNQ                QEV
        cggggaacggtgggccaacggtagcggatagacac                cgggccacaagatgaacggaatagacacac                cgg
        catttggaactcccgtgtaaatacacaaaaaaaaa                taaagggaatctgagtaagagaagatataa                aat
        ttggaaggatgaatccggggagtaaaaacaagaag                gggggggggccgggcggaggccaaccagtg                aaa
                                                                                                            

Query   SAASSASAVPKSKPNKKPLRGGG <---Intron---> YNPLSGEGGGTCSWRPGRRGPSAGGUG
           /||||||||||||||||||| <   1950bp   > |||||||||||||||||||||||||||
Target  EPGASASAVPKSKPNKKPLRGGG                YNPLSGEGGGTCSWRPGRRGPSAGGUG
        gcggtgtggcatacaaactaggg                tacctgggggatttacgccgctgggtg
        acgccccctcacacaaactggg                gaactcgagggcgcggcggggcccgggg
        attcgcaacgagagcagcgaat                ctccgtaaaaggccggccggccaataac
                                                                        * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 556 ; UGA-SECIS: 559

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = + Positions = 52818 - 52906
 Found by:  Infernal (score=22.29) Covels (score=37.04)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -12.02

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