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

 Blastx evalue: 2e-17
 Query name: gi|67191194|ref|NP_001019905.1| selenoprotein S [Gallus gallus]
 Query range: 30-194  (total 194)

 Target: /data/www-rg/seblastian_results/710819280/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: -
 Positions:
 -Exon 1  55794        55929
 -Exon 2  53984        54090
 -Exon 3  52298        52387
 -Exon 4  52109        52187
 -Exon 5  49888        49973

 Redox box: no

Query   VGALLSSYGWYILLACVAIYLIVQKISPYLRMRPSSQQGATGAAVE <---Intron---> PDMVVRRQEALLASRLRMQEELNAQAERYKEKQRQ <-
        ||/||/||||| | ||||/||/|||//  /| /  |/  |||| /| <   1703bp   > ||/|||||||| |/| ||||/|| |||//|||||| < 
Target  VGSLLASYGWYFLFACVAVYLLVQKLAEKMRAQRRSRPHATGALLE                PDVVVRRQEALAAARFRMQEQLNEQAEKFKEKQRQ   
        ggtccgatgtttctgtgggtccgcacggaaagcaaacccgaggccg                cggggaccggcgggctaacgctagcggatagacac   
        tgcttcgaggatttcgtctatttaatcaatgcaggggcaccgctt                acatttggaactcccgtgtaaataaacaataaaaga   
        gcgggccccgcccccccccccctgggaaggatgggcgctatgggt                attgggaggatgaatccggagggtaataacaagaag   
                                                                                                            

Query   --Intron---> LEEQKRRQKIEMWESMQEGKSYKGNLKLSQ <---Intron---> QEAESGASTSSAVPKSKPNKKPLRGGG <---Intron---
          1596bp   > |||/|||||/ |||||||||||||||| || <   110bp    > || || || || ||| ||||||||||  <   2135bp   
Target               LEEEKRRQKVAMWESMQEGKSYKGNLKRSQ                QEIESAASPSSTVPKPKPNKKPLRGGS              
                     cgggaaacaggatgaacggaatagacacac                cgagtggtcttagcacacaaactcgga              
                     taaaaggaatctgagtaagagaagatagga                aatacccccccctcacacaaactggg               
                     taaggagagacggacgaaaactaatgagcg                aaaactttcgaacggtatcagtgaat               
                                                                                                            

Query   > YNPLSGEGGGTCSWRPGRR-GPSAGGUG
        > ||||||||||||/|||||| |||/||||
Target    YNPLSGEGGGTCAWRPGRRGGPSSGGUG
          tacttgggggatgtacgcaggcttggtg
         gaactcgagggcgcggcgggggcccgggg
         ttttgtaactacttgaatcactctataac
                                    * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 845 ; UGA-SECIS: 848

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = - Positions = 49042 - 48962
 Found by:  Infernal (score=22.01) Covels (score=34.13)
 Stem2 length = 10   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -11.17

         ..(((((((.......(((((((((((((((.................)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ..([([((((......{[[{(({((((((((.................))))))))}))}]]}......-..))))])])..
 target  GACAAGCUGCACUGAAUGAUGUUGUCCUUAUAAAUGGUAAACAAACCAGUGAGGAUCACUGAUACUAGA-CAGUAGAUGGGG
                         ****           ^^^                         ****