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

 Blastx evalue: 1e-22
 Query name: gi|992212532|ref|XP_007250722.2| PREDICTED: selenoprotein T1a-like [Astyanax mexicanus]
 Query range: 1-193  (total 193)

 Target: /data/www-rg/seblastian_results/461442420/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: +
 Positions:
 -Exon 1  50003        50133
 -Exon 2  51351        51461
 -Exon 3  51686        51812
 -Exon 4  52128        52215
 -Exon 5  52353        52474

 Redox box: YES

Query   MRWLALSVLAVWLCAFSSAAGESTGVKKMKMQFATGPLLKFQIC <---Intron---> ISUGYKRVFEEYTQALYQRYPDIRIEGENYLPLPVYR <-
        |||||||||||||||||||||||||||||||||||||||||||| <   1217bp   > ||||||||||||||||||||||||||||||||||||| < 
Target  MRWLALSVLAVWLCAFSSAAGESTGVKKMKMQFATGPLLKFQIC                ISUGYKRVFEEYTQALYQRYPDIRIEGENYLPLPVYR   
        acttgctgcggtctgttaggggaaggaaaaactgagcccatcat                attgtacgtggtacgctcctcgacagggatccccgta   
        tggtctcttctgtgctcgccgagcgtaatatatccgcttatatg                tcggaagttaaacactaagacatgtagaaatctctag   
        gtgagggttgggtcgtcctcagcgatagggggcccgatcacgc                tccagcgggtggcggtgcggcaccctgagctttgttc    
                                                                      *                                     

Query   --Intron---> YIASFLSIFKLLLIGVIVVGKDPFALFGMQAPGLWVWSQENK <---Intron---> IYACMMVFFFSNMIENQCMSTGAFEIKLN
          224bp    > |||||||||||||||||||||||||||||||||||||||||| <   315bp    > |||||||||||||||||||||||||| ||
Target               YIASFLSIFKLLLIGVIVVGKDPFALFGMQAPGLWVWSQENK                IYACMMVFFFSNMIENQCMSTGAFEITLN
                     tagttctatacccaggagggagctgctgacgcgctgtacgaa                atgtaagtttaaaagactataggtgaaca
                     atccttcttattttgttttgaactcttgtaccgtgtggaaaa                tacgttttttgattaaagtccgctatcta
                    gtttctgttcagggtagttgggcactcctgaaaatgtgtaatg                atctgggcccctgtacgcgtatttacgct
                                                                                                            

Query   D <---Intron---> VPVWSKLESGHLPSMQQLVQILENEMKLNVHMDRLPHHHS
        | <   137bp    > ||||||||||||||||||||||||||||||||||||||||
Target  D                VPVWSKLESGHLPSMQQLVQILENEMKLNVHMDRLPHHHS
        g                gcgttacgtgccctacccgcacgagaacagcagaccccct
                        atctgcatacgatcctaattattaaatatatatagtcaaac
                        ttgggcgggctcgtcggggggcggtagggtgcgcatactcc
                                                                 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 1011 ; UGA-SECIS: 1449

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = + Positions = 53486 - 53566
 Found by:  Infernal (score=30.55) Covels (score=32.28)
 Stem2 length = 11   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -22.81

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