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

 Blastx evalue: 6e-65
 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/105772402/tempfiles/temptarget.fasta
 Chromosome: OMLM01009182.1:subseq_42932,79327_ Strand: -
 Positions:
 -Exon 1  52438        52507
 -Exon 2  52133        52309
 -Exon 3  51387        51485
 -Exon 4  51190        51282
 -Exon 5  50946        51102
 -Exon 6  50729        50844
 -Exon 7  50454        50531
 -Exon 8  50172        50311
 -Exon 9  49991        50080

 Redox box: no

Query   MMASALANRAIGAIVGSAVADAAA <---Intron---> QPLHWVYDLQKLKGILALNPNPEFHPESANPFYRRETGKQSCYGDQAYVLLESLSECGG 
         ||/|| /|||||||||||||||| <   128bp    > ||||||||||||/ ||| /  |||  |||||||||/||/|||||||||||||||||||| 
Target  QMATALVDRAIGAIVGSAVADAAA                QPLHWVYDLQKLQEILAQDLYPEFRSESANPFYRRKTGQQSCYGDQAYVLLESLSECGG 
        cagagcggagaggaggtggggggg                cccctgtgccaccgacgcgctcgtctgtgacttaaaagccattggcgtgccgtctgtgg 
        atcccttagctgcttgcctcacc                cactagtaataataattcaatacatgcaccactaggacgaaggagaacatttactcagg  
        ggtatgccaaaactaaattgtaa                ggcccggcctggtggtgtgtgccacgtattcaccgggacggcccacggtcgggcgtata  
                                                                                                            

Query   <---Intron---> LNVDDLKQRTLKVFGPGSEYDTPVNDPYRERGG <---Intron---> PRPQLPIDGPWRHASLKSFLKNVDAGKEETG <---
        <   647bp    > |/|/||||| || ||||||||||||||||/||| <   104bp    > |||||||/||||||||||||||/|||||||| <   
Target                 LDVEDLKQRMLKFFGPGSEYDTPVNDPYRDRGG                PRPQLPIEGPWRHASLKSFLKNMDAGKEETG     
                       cggggcaccacattgcgtgtgacgagctagagg                caccccaggctacgataattaaagggaggag     
                      gtataataagttattgcgcaaacctaacagagg                gcgcatctagcggacgtagttaatacgaaac      
                      gattatgggcgggctgaaaatcaactttcacaa                gaatggccgacgatatagctggcgtgcagga      
                                                                                                            

Query   Intron---> CENDCQIDGIAKLAPIVAFYAGQPDMLEKVEQAIRVTQNNDECVAETLAAAR <---Intron---> FLEHFILNGPDPKALDAVLNQ
         87bp    > |//|||||||||||||||||||/||||||||||/||||||| |||||||||| <   101bp    >  |||||||||||  |//||||
Target             CQDDCQIDGIAKLAPIVAFYAGKPDMLEKVEQAVRVTQNNDACVAETLAAAR                LLEHFILNGPDPNVLESVLNQ
                   tcggtcaggagacgcaggttggacgacgaggcggcgacaaggtgggacggga                ccgctacagcgcagtgtgcac
                  ggaaagatagtcatccttctacgacattaataactgtcaaaacgtcactcccg                ttaatttagcacattacttaa
                  ccgcctgttaacagttcggtcaagtcggagtagcctttgcttatgaatgata                gcggtctcttttatcgggggtg
                                                                                                            

Query   LNDPNRKQPQDLDKAVIG <---Intron---> HIHQVKENLSKTPQKLIPSVFTNAUG <---Intron---> LPGAFQAALHGVLTATRYETAVKD
        |/| ||||||||||/| | <   197bp    > ||/||||||||| //|||||| | || <   142bp    > ||||||||||||||| /|| |//|
Target  LSDKNRKQPQDLDKSVTG                HIYQVKENLSKTHRELIPSVFPNTUG                LPGAFQAALHGVLTAKKYEQAIRD
        cagaaaacccgcgatgag                catcgagattaaccgcactgtcaatg                tcggtcggccggtagaatgcgaag
        tgaaagaacaataactc                gataataaatcacagattccttcacg                gtcgctacctagttccaaaaactga
        atcacaggcacgcaact                gtttggggtacgttagaccattacta                tgttgcaaggtacgatggcggtcgc
                                                                  *                                         

Query   TMSCGGCTCSRGSFIGACLGAQ <---Intron---> VGLEGIPESWKSKTLQYDLVLEHAKKITKH
        |||||||||||||||||||||| <    91bp    > /|||||| |||||||/|| |||||||||||
Target  TMSCGGCTCSRGSFIGACLGAQ                IGLEGIPSSWKSKTLRYDSVLEHAKKITKH
        aaatggtatacgttaggtcggc                agcggactttataacctgtgtgcgaaaaac
        ctgggggcggggcttgcgtgca                tgtagtcccgacactgaacttaacaatcaa
        cgctgaccccaacctcatcgag                tatgatatcggcacgaccagggtcggacat
                                                                            
 Sequence until next stop: 
CACACATAG
 H  T  * 

 Distance CDS-SECIS: 65 ; UGA-SECIS: 296

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = OMLM01009182.1:subseq_42932,79327_ Strand = - Positions = 49925 - 49848
 Found by:  Infernal (score=30.71) Covels (score=22.15)
 Stem2 length = 11   Apical loop length = 11   Insertion in stem2 = 0, 0
 Free Energy = -19.13

         ..(((((((.........(((((((((((((((................)))))))))))))))...........)))))))..
 model   uucggucaugcg--UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuu--u-uuucaugaccggc
         (((({(((((........{[[{(((((((((((.........-----..)))))))))))}]]}.......-..)))))}))))
 target  CUUUCACAGGACAGUGAAUGAAGGUUCUUGUCUAAACUGUUG-----GAAGGCAGGAAUCAGAUGCUUUUG-UCUCUGUUGAAG
                           ****           ^^^                        ****