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

 Blastx evalue: 5e-50
 Query name: gi|1025438331|ref|XP_007552619.2| PREDICTED: crystallin J1A-like [Poecilia formosa]
 Query range: 1-340  (total 341)

 Target: /data/www-rg/seblastian_results/735890388/tempfiles/temptarget.fasta
 Chromosome: KV884754.1:subseq_1752858,100000_ Strand: +
 Positions:
 -Exon 1  48578        48644
 -Exon 2  48935        49111
 -Exon 3  50001        50099
 -Exon 4  50202        50294
 -Exon 5  50378        50534
 -Exon 6  51288        51403
 -Exon 7  51587        51664
 -Exon 8  51841        51980
 -Exon 9  52067        52159

 Redox box: no

Query   MTSVVANRAVGAIVGSAVADAAA <---Intron---> QPLHWVYDLQKLKGILAQDPNPEFRSESANPFYRRQTGQQSCYGDQAYVLLESLSECGG <
        | / / /||||||||/||||||| <   290bp    > ||||||||| ||/ ||||||||||||||||||||||||/|||||||||||||||| ||| <
Target  MAAALVDRAVGAIVGAAVADAAA                QPLHWVYDLPKLQKILAQDPNPEFRSESANPFYRRQTGEQSCYGDQAYVLLESLSVCGG  
        agggcggaggggagggggggggg                cccctgtgccaccaacgcgcacgtctgtgacttaacaggcattggcgtgccgtctgtgg  
        tcccttagctgcttgcctcacc                cactagtaatcataattcaacacatgcaccactaggacgaaggagaacatttactctgg   
        gtatgccaacgctaaattataa                agtccggtccggaggtgtgtactacctatccgccgggacggcctacggtcgggcgtata   
                                                                                                            

Query   ---Intron---> LNVDDLKQRTLKFFGPGSEYDTPVNDPYRDRNG <---Intron---> PRPQLPIEGPWRQASLKSFLKNVDAGKEETG <---I
           889bp    > |/|/||||||||||||||||||||||||| | | <   102bp    > ||||||||||||||||||||||||||||||| <    
Target                LDVEDLKQRTLKFFGPGSEYDTPVNDPYRQRGG                PRPQLPIEGPWRQASLKSFLKNVDAGKEETG      
                      cggggcaccacattgcgtgtgacgagctacagg                caccccaggctacgataatcaaggggaggag      
                     gtataataagctattgcgcaaacctaacagagg                gcgcatctagcggacgtagttaatacgaaac       
                     tattatgaacagactacaagtcatctttcggaa                gaatgtccggagagatagccgatgttcagga       
                                                                                                            

Query   ntron---> CETDCQIDGIAKLAPIVAFYAGQPDMLEKVEQAIRVTQNNDECVAETLAAAR <---Intron---> FLEHFILTGPDPNVVDVVLNQL
        83bp    > ||/|||||||||||||||||||  ||||||||||||||||| |||||||||| <   753bp    > ||||||| ||||  /| ||/||
Target            CESDCQIDGIAKLAPIVAFYAGNTDMLEKVEQAIRVTQNNDACVAETLAAAR                FLEHFILNGPDPKALDAVLDQL
                  tgagtcaggagacgcaggttggaagacgaggcgacgacaaggtgggacggga                tcgctacagcgcagtgggcgcc
                 ggagagatagtcatccttctacgacattaataactgtcaaaacgtcactcccg                ttaatttagcacactacttaat
                 ctgcccgttaatagttaggtcgattcggaagagcctcagctcgtgagtgaaa                gcggtccgttttcacatagttgc
                                                                                                            

Query   SDPSRKQPQDLDKAVIG <---Intron---> HIHQVKENLSKRPQELIPAVFPNTUG <---Intron---> LPGAFQAALHGVLTAEHFEAAIRDT
        || /|||||||||/| | <   183bp    > || |||||||| |||/||/|| |||| <   176bp    > ||||||||||| |||  /| |||||
Target  SDRNRKQPQDLDKSVTG                HIQQVKENLSKTPQEIIPSVFTNTUG                LPGAFQAALHGALTATQYEQAIRDT
        agaaaacccgcgatgag                caccgagattaaccgaacagtaaatg                tcggtcggccggcagactgcgaaga
        gagagaacaataactc                gataataaatcaccaattcgttcacg                gtcgctacctagctcccaaaactgac
        tcgcgggcgcgcaact                gccaggggtacgttggatctgttcta                tgatacaaggtacgacagtagttacc
                                                                 *                                          

Query   MSCGGCTCSRASFIGACVGAQ <---Intron---> IGLEGIPASWLSKTSRSNSVLAHAKKIASHH
        |||||||||| ||||||/||| <    86bp    >  ||||||/|| ||| |  ||| ||| |  ||
Target  MSCGGCTCSRGSFIGACLGAQ                FGLEGIPSSWTSKTLRYGSVLEHAKTITKHH
        aatggtatacgttaggtcggc                tgcggactttataacctgtgtgcgaaaaacc
        tgggggcggggcttgcgtgca                tgtagtcccgccactgagcttaacactcaaa
        gctgaccccaacctgattgcg                tgtgattccgacacgatctggatcggacacc
                                                                            
 Sequence until next stop: 
CAGTAG
 Q  * 

 Distance CDS-SECIS: 65 ; UGA-SECIS: 299

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KV884754.1:subseq_1752858,100000_ Strand = + Positions = 52225 - 52297
 Found by:  Infernal (score=32.3) Covels (score=24.86)
 Stem2 length = 10   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -19.72

         ..(((((((.......(((((((((((((((................)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         ..((([((((--....{[[{((((((((((..........-----...))))))))))}]]}......-..))))])))..
 target  CACAGAACAG--UGGAUGAAGGUUCUUGUCUAAACUGCUG-----GAUGGCAGGAGCCAGAUGUUUUU-GUCUGUGUUGAA
                         ****           ^^^                        ****