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

 Blastx evalue: 3e-10
 Query name: gi|992184532|ref|XP_007238827.2| PREDICTED: crystallin J1A-like [Astyanax mexicanus]
 Query range: 1-342  (total 342)

 Target: /data/www-rg/seblastian_results/678548897/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: -
 Positions:
 -Exon 1  56690        56756
 -Exon 2  55343        55521
 -Exon 3  50008        50164
 -Exon 4  49746        49825
 -Exon 5  41519        41650

 Redox box: no

Query   MALSVADRAAGAIIGSAVADAAA <---Intron---> QPMHWVYNLQQLEEYLADDPEPEFRSESVNPFYRRETGRQSCYGDQSYVLLESLSECRG <
        ||||||||||||||||||||||| <   1168bp   > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| <
Target  MALSVADRAAGAIIGSAVADAAA                QPMHWVYNLQQLEEYLADDPEPEFRSESVNPFYRRETGRQSCYGDQSYVLLESLSECRG  
        agctgggcggggaagtggggggg                ccactgtaccccggtcgggcgcgtctgtgacttaagagccattggcatgccgtctgtag  
        tctctcagccgcttgcctcacc                cactagtaataataaatcaacacatgcactactaggacggaggagaagatttactcaggg  
        ggggctccccggtccacgccta                tgggcgttcgggggatgcttgaggcgcgggtgccggaccggcccatgcctggggccgcat  
                                                                                                            

Query   ---Intron---> LDVEDLKRRVYGFFGPGSEYDSPVNDPYRDKGAPRPQLPIEGPWRQASLKSFIRNVDSGKSETGCDSDVQMDGVARLAPIVAFYAG
           5178bp   >                                                                                       
Target                --------------------------------------------------------------------------------------
                      --------------------------------------------------------------------------------------
                      --------------------------------------------------------------------------------------
                      --------------------------------------------------------------------------------------
                                                                                                            

Query   KPEMLEKVEDSVRVTQNNDQSVAVTLAAARFLEHFILNGADPEVLPTVLKQLNDPNRTNPQDLDKAVAG <---Intron---> QIQEVKENLSKSQKE
                        | / |      / |||||||||||||||||||||||||||||||||||||||| <   182bp    > |||||||||||||||
Target  ----------------NFESSTDSKFCSERFLEHFILNGADPEVLPTVLKQLNDPNRTNPQDLDKAVAG                QIQEVKENLSKSQKE
        ----------------atgaaagaatttgatcgctacagggcggccagcaccagcaaaaccgcgagggg                cacggagacaatcag
        ----------------ataggcagatgcagttaatttagcacattccttaataacagcacaataactc                gataataaatgacaaa
        ----------------ttgcttctgcttagcggcttgctttagcgcccgggcccccgacagtgcatat                aatgaggatgtacggg
                                                                                                            

Query   LIPAVFTNTUR <---Intron---> LPGAFQAALHGVLTAAGFEEAVRNTMSCGGCTCSRSSFIGACIGAQVGVEGIPESWKSRTLRYSSLLELTEIT
        ||||||||||| <   8095bp   >                                       |  |/  ||||||||||||||||||||||||||||
Target  LIPAVFTNTUR                -----------------------------------DGIIMGCVCLQVGVEGIPESWKSRTLRYSSLLELTEIT
        cacggtaaatc                -----------------------------------ggaaagtgttcgggggacgttaacacatatccgcagaa
        ttccttcacgg                -----------------------------------agtttggtgtatgtagtcacgaggctgagcttatcatc
        gttagtcccat                -----------------------------------tgttgacgtggcttggtgggggtgtgaccaaggctgct
                 *                                                                                          

Query   TGSERV
        ||||||
Target  TGSERV
        agtgcg
        cgcagt
        taagag
              
 Sequence until next stop: 
TGA
 * 

 Distance CDS-SECIS: 29 ; UGA-SECIS: 164

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = - Positions = 41489 - 41423
 Found by:  Infernal (score=24.09) Covels (score=16.64)
 Stem2 length = 10   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -13.62

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((---....{[[(((((([((((..........-----...))))]))))))]]}----....)))))))..
 target  UAAGAACAG---UUUAUGAUGGUUCAGACUGAAAUCUGUG-----UAAAGUCGGAACUGGAU----UCAUUUGUUUUGU
                         ****           ^^^                        ****