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

 Blastx evalue: 7e-38
 Query name: gi|928031856|ref|XP_013864403.1| PREDICTED: crystallin J1A-like [Austrofundulus limnaeus] >gi|928031858|ref|XP_013864404.1| PREDICTED: crystallin J1A-like [Austrofundulus limnaeus]
 Query range: 2-340  (total 341)

 Target: /data/www-rg/seblastian_results/196075256/tempfiles/temptarget.fasta
 Chromosome: SSNR01000266.1:subseq_316700,108101_ Strand: +
 Positions:
 -Exon 1  47322        47385
 -Exon 2  50068        50244
 -Exon 3  50380        50478
 -Exon 4  50577        50669
 -Exon 5  50747        50903
 -Exon 6  51297        51412
 -Exon 7  57644        57721
 -Exon 8  57798        57937
 -Exon 9  58006        58098

 Redox box: no

Query   ASSVANRAVGAIVGSAVADAAA <---Intron---> QPLHWIYDLQKLKEILAQDPNPEFRPESANPFYRRQTGQQSCYGDQAYVLLESLSECGG <-
        /|/|||||/||||||||||||| <   2682bp   > |||||/||||||||||||||||||| ||||||||||||||||||||||||||||| ||| < 
Target  SSAVANRAIGAIVGSAVADAAA                QPLHWLYDLQKLKEILAQDPNPEFRSESANPFYRRQTGQQSCYGDQAYVLLESLSACGG   
        ttgggaagaggaggtggggggg                cccctttgccacagatgcgcacgtctgtgacttcccagccattggcgtgccgtctgtgg   
        ccctcagctgcttgcctcacc                cactagtaataataattcaacacatgcaccactaggacgaaggagaacatttactccgg    
        aatgccacaaccaaattatta                ggtacggctcgggggtgtgtaccgtctgtccgccagggtggcccacgcccgggccacta    
                                                                                                            

Query   --Intron---> LNVDDLKQRTLKYFGPGSEYDTPVNDPYRDRGG <---Intron---> PRPQLPIDGPWRQASLKSFLKNVDAGKEETG <---In
          135bp    > |||||||/||| /|||||||||||||||||||| <    98bp    > |||||||/||||||||||||||||||||||| <    7
Target               LNVDDLKRRTLDFFGPGSEYDTPVNDPYRDRGG                PRPQLPIEGPWRQASLKSFLKNVDAGKEETG       
                     cagggcaccacgttgcgtgtgacgagctcgagg                caccccaggctacgacaatcaaggggaggag       
                    gtataataggctattgcgcaaacctaacagagg                gcgcatctagcggacgtagttaatacgaaac        
                    tattctaggtagcctaaaagtctcccttcacga                gggtggccgaggagctggccggtcctggggg        
                                                                                                            

Query   tron---> CETDCQIDGIAKLAPIVAFYAGQPDMLDKVEQAVRVTQNNDEXVAETLAAAR <---Intron---> FLEHFILNGPDPKVLEVVLTQLS
        7bp    > |||||||||||||||/|||||||||||/|||||||||||||| ||||||||| <   393bp    > ||||||||| ||/||/||| |||
Target           CETDCQIDGIAKLAPVVAFYAGQPDMLEKVEQAVRVTQNNDECVAETLAAAR                FLEHFILNGSDPRVLDVVLKQLS
                 tgagtcaggagacgcgggttggccgacgaggcggcgacaaggtgggacggga                tcgctacagtgcagcgggcacca
                ggacagatagtcatccttctacgacattaataactgtcaaaaagtcactcccg                ttaatttagcacgttatttaatg
                atgtctgtcaacgattagtttaagccggagtggctcccacctgtaaatgtag                gtggtcctttatcatgcgtaggct
                                                                                                            

Query   DLNRKQPQDLDRAVTG <---Intron---> HIHQVKENLSRSPQELIPTVFPNTUG <---Intron---> LPGAFQAALQGVLTARHFETAIRDTM
        | ||| |||||||| | <   6231bp   > ||||/|||||//|||||||||||/|| <    76bp    > ||||||||| |||||/|||||/||||
Target  DPNRKHPQDLDRAVAG                HIHQIKENLSKTPQELIPTVFPNSUG                LPGAFQAALHGVLTAQHFETAVRDTM
        gcaaacccgcgagggg                caccaagactaaccgcacagtcattg                tcggtcggccggcagcctgaggagaa
        acagaacaatagctc                gataataaatcaccaattccttcacg                gtcgctacctagttccaatacctgact
        cacaaccgtgcaact                tcccgaggtaagtaggctcggcacaa                gaatgcgaggtacgacgctggccaccg
                                                                *                                           

Query   SCGGCTCSRASFIGACLGAQ <---Intron---> IGLEGIPASWISRTLRLNSVLEHGKRITEHH
        |||||||||||||||||||| <    68bp    > ||/||/||||/| ||| /||||| |//|/||
Target  SCGGCTCSRASFIGACLGAQ                IGIEGVPASWMSNTLRCSSVLEHAKKVTKHH
        atggtataagttaggtcggc                agagggcgttaaaacctatgcgcgaagaacc
        gggggcgggccttgcgtgca                tgtagtcccgtgactgggcttaacaatcaaa
        ctggccccaacccagtcatg                tgtaattagggcccgcctgggatcgggcacc
                                                                           
 Sequence until next stop: 
CAGTAG
 Q  * 

 Distance CDS-SECIS: 39 ; UGA-SECIS: 273

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = SSNR01000266.1:subseq_316700,108101_ Strand = + Positions = 58138 - 58212
 Found by:  Infernal (score=34.52) Covels (score=23.15)
 Stem2 length = 10   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -16.81

         ..(((((((.......(((((((((((((((................)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ...((((((.......{[[{((((((((((..........-----...))))))))))}]]}......-...))))))...
 target  UUUGCAGAGCGGUGAAUGAAGGCUUUUGUCUAAACGUACA-----GGCGAUGGAAGCCAGAUGUUGUU-UGUCUCUGUUCA
                         ****           ^^^                        ****