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

 Blastx evalue: 1e-48
 Query name: gi|908520312|ref|XP_013120966.1| PREDICTED: crystallin J1A-like isoform X1 [Oreochromis niloticus]
 Query range: 1-340  (total 343)

 Target: /data/www-rg/seblastian_results/618526994/tempfiles/temptarget.fasta
 Chromosome: WARS01000030.1:subseq_3428277,200000_:subseq_0,120000_ Strand: +
 Positions:
 -Exon 1  99152        99221
 -Exon 2  99425        99601
 -Exon 3  100001       100099
 -Exon 4  100211       100303
 -Exon 5  100389       100545
 -Exon 6  100820       100935
 -Exon 7  101203       101280
 -Exon 8  101421       101560
 -Exon 9  101655       101744

 Redox box: no

Query   MMASALANRAIGAIVGSAVADAAA <---Intron---> QPLHWVYDLQKLKGILALNPNPEFHPESANPFYRRETGKQSCYGDQAYVLLESLSECGG 
         || |||/|||||||||||||||| <   203bp    > |||||||/||||/|||| /||||| ||||||||||/||/||||||||/|||||||| || 
Target  QMAVALADRAIGAIVGSAVADAAA                QPLHWVYNLQKLQGILAQDPNPEFRPESANPFYRRQTGQQSCYGDQAFVLLESLSEYGG 
        cagggcggagaggaggtggggggg                cccctgtaccaccgacgcgcacgtccgtgacttaacagccattggcgtgccgtttgtgg 
        atctctcagctgcttgcctcacc                cactagtaataatagttcaacacatgcaccactaggacgaaggagaacttttactcaag  
        ggtatgccagaaccgaacgacga                ggcccggctcgggggcgtgtactgcctgggctccggggcagcccccgatcgggcgtatc  
                                                                                                            

Query   <---Intron---> LNVDDLKQRTLKVFGPGSEYDTPVNDPYRERGG <---Intron---> PRPQLPIDGPWRHASLKSFLKNVDAGKEETG <---
        <   399bp    > |||||||||||| |||||||||||||||||||| <   111bp    > |||||||/||||| ||||||||||||||||| <   
Target                 LNVDDLKQRTLKFFGPGSEYDTPVNDPYRERGG                PRPQLPIEGPWRHGSLKSFLKNVDAGKEETG     
                       cagggcaccacattgcgtgtgacgagctagcgg                caccccaggctacgataatcaaggggaggag     
                      gtataataagctattgcgcaaacctaacagagg                gcgcatctagcggaggtagttaatacgaaac      
                      tactttgggctggctgtgagccgttcttcagaa                gagtggctgaagatgtagccggtgtaaggga      
                                                                                                            

Query   Intron---> CENDCQIDGIAKLAPIVAFYAGQPDMLEKVEQAIRVTQNNDECVAETLAAAR <---Intron---> FLEHFILNGPDPKALDAVLNQ
         85bp    > || ||||||||||||||||||||||||||||||/|||||||||||||||||| <   274bp    > ||||||||||||||||/||/|
Target             CETDCQIDGIAKLAPIVAFYAGQPDMLEKVEQAVRVTQNNDECVAETLAAAR                FLEHFILNGPDPKALDSVLDQ
                   tgagtcaggagacgcaggttggccgacgaggcggcgacaaggtgggacggga                tcgctacagcgcagtgtgcgc
                  ggacagatagtcatccttctacgacattaataactgtcaaaaagtcactcccg                ttaatttagcacactacttaa
                  ctgcctgttaacagttagtttaaatcggggcggtctcagcttatgagcgatc                gcggtccgccttaacgctgctg
                                                                                                            

Query   LNDPNRKQPQDLDKAVIG <---Intron---> HIHQVKENLSKTPQKLIPSVFTNAUG <---Intron---> LPGAFQAALHGVLTATRYETAVKD
        |/|||||||||||||||| <   267bp    > ||||||||||||||/|||/|| | || <   140bp    > |||||||||||||||  /| ||/|
Target  LSDPNRKQPQDLDKAVIG                HIHQVKENLSKTPQELIPTVFPNTUG                LPGAFQAALHGVLTAKHFEQAVRD
        cagcaaacccgcgaggag                caccgagattaaccgcacagtcaatg                tcggtcggccggcagactgcggag
        tgacagaacaataactt                gataataaatcaccaattccttcacg                gtcgctacctagttccaataactga
        ctcgcaggcgtgcagct                gcttggggtaagttgggcctgtacaa                tgatgcaaggtacgacactggtcat
                                                                  *                                         

Query   TMSCGGCTCSRGSFIGACLGAQ <---Intron---> VGLEGIPESWKSKTLQYDLVLEHAKKITKH
        |||||||||||||||||||||| <    94bp    > /|||||| || ||||/|/ |||||||||||
Target  TMSCGGCTCSRGSFIGACLGAQ                IGLEGIPTSWTSKTLRYETVLEHAKKITKH
        aaatggtataagttaggtcggc                agcggacattataacctgagtgcgaaaaac
        ctgggggcggggcttgcgtgca                tgtagtcccgccactgaacttaacaatcaa
        cgctgacctcaacctacttttg                tatgataacggcacgttgcgggtcggacac
                                                                            
 Sequence until next stop: 
CACCAATAG
 H  Q  * 

 Distance CDS-SECIS: 77 ; UGA-SECIS: 308

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = WARS01000030.1:subseq_3428277,200000_:subseq_0,120000_ Strand = + Positions = 101822 - 101895
 Found by:  Infernal (score=37.67) Covels (score=22.55)
 Stem2 length = 11   Apical loop length = 11   Insertion in stem2 = 0, 0
 Free Energy = -22.56

         ..(((((((.......(((((((((((((((................))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         (({((((((.......{[[{(((((((((((.........-----..)))))))))))}]]}.....-...))))))}))
 target  UUCACAGAGCAGUGAAUGAAGGUUCUUGUCUAAACUGUAG-----GAAGACAAGAGCCAGAUGUUUU-UGUCUCUGUUAA
                         ****           ^^^                        ****