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

 Blastx evalue: 3e-30
 Query name: gi|930749619|ref|XP_005933732.2| PREDICTED: crystallin J1A-like isoform X1 [Haplochromis burtoni]
 Query range: 30-368  (total 372)

 Target: /data/www-rg/seblastian_results/83701965/tempfiles/temptarget.fasta
 Chromosome: OMLM01014617.1:subseq_0,91592_ Strand: -
 Positions:
 -Exon 1  42249        42318
 -Exon 2  41415        41594
 -Exon 3  40296        40394
 -Exon 4  39685        39777
 -Exon 5  38854        39010
 -Exon 6  38647        38762
 -Exon 7  37494        37571
 -Exon 8  36609        36748
 -Exon 9  35361        35447

 Redox box: no

Query   RMASALANRAMGAITGSAVADAAA <---Intron---> QPLHWVYDLQKLKGILA-LNPNPEFHPESANPFYRRETGKQSCYGDQAYVLLESLSECGG
        /|| //|/|//||| |/||||||| <   654bp    > ||/||/|/  /|| /|/ | | |||  /||||||||/||/|/||||||||||||||/|| 
Target  QMALSVADRSIGAIIGAAVADAAA                QPMHWIYNPDQLKEVLSDLEPCPEFRSQSANPFYRRKTGEQTCYGDQAYVLLESLSQCGD
        cagtagggataggaaggggggggg                ccactatacgccaggctgcgctcgtctctgacttcaaaggcattggcgtgccgtcactgg
        atctgtcagctgcttgcctcacc                cactagtaacaataattcatacgcatgcaccactaggacgaacgagaacatttactgagg 
        ggcgcgacactgctcgaagataa                cgcgcgcctacgcaatgttggcctgtgtgagtccccgaacgagctttgaccgggagtgta 
                                                                                                            

Query    <---Intron---> LNIDDLKQRTLKVFGPGSEYDTPVNDPYRERGG <---Intron---> PRPQLPIDGPWRHASLKSFLKNVDAGKEETG <--
         <   1020bp   > ///||| /|  | ||||/ || |||||||//|| <   518bp    > |/  ||||||||/||||/|//|||||||||| <  
Target                  VDVDDLIKRMYKFFGPGTVYDLPVNDPYRKKGG                PKAILPIDGPWRNASLKAFIRNVDAGKEETG    
                        gggggtaacatattgcgagtgccgagctaaagg                cagaccaggctaagacagtaaaggggaggag    
                       atataattagtaattgcgctaatctaacagaag                gcacttctagcggacgtacttgatacgaaac     
                       tgtaccgcacgcgctcaaagctttcttacgaaa                tcaccctttcagacacgatccatgttcaaat     
                                                                                                            

Query   -Intron---> CENDCQIDGIAKLAPIVAFYAGQPDMLEKVEQAIRVTQNNDECVAETLAAAR <---Intron---> FLEHFILNGPDPKALDAVLN
         674bp    > || ||||||| || |/|| |||/ /||||||/||||||||| ||| |||||| <    91bp    > |||||||||||| |||||| 
Target              CEVDCQIDGITKLTPVVAMYAGRSEMLEKVEKAIRVTQNNDMCVAVTLAAAR                FLEHFILNGPDPNALDAVLA
                    tgggtcaggaaacacgggatggctgacgaggagacgacaagatgggacggga                ttgctacagcgcagcgggcg
                   ggatagatagtcatccttctacggcattaataactgtcaaaatgtctctcccg                ttaatttagcacactacttc
                   ctagctgatcctggtaggcgctagtggggaggacaaccgttcgtgtgatttg                gtggtctgtcttcttgtttgt
                                                                                                            

Query   QLNDPNRKQPQDLDKAVIG <---Intron---> HIHQVKENLSKTPQELIPSVFTNAUG <---Intron---> LPGAFQAALHGVLTATRYETAVR
        |||||||/ ||/||/|||  <   1075bp   > ||||||/|||/| |//||/|||| |  <   745bp    > |||||| ||||||| |/ / |||
Target  QLNDPNRQNPQELDQAVIA                HIHQVKDNLSRTSQQIIPAVFTNTUA                LPGAFQGALHGVLTLTQLDEAVR
        ccagcaacaccgcgcggag                caccgagactaatccaacggtaaatg                tcggtcggccggcacaccgggga
        ataacagaacaataactt                cataataaatcgccaattccttcacg                ctcgctagctagttctcataactg
        gcttacagctaggcgtac                acccgggccacgacggcattgcacaa                tgttacgagttacgagcggtaacg
                                                                   *                                        

Query   DTMSCGGCTCSRGSFIGACLGAQ <---Intron---> VGPEGIPESWKSKTLQYDLVLEHTKKITK
        |||  |||| || |||||| ||| <   1161bp   >  |  ||||||  /||/| |/||  / / |
Target  DTMRRGGCTASRASFIGACFGAQ                TGLHGIPESWMKRTLRYPLLLELAQNLVK
        gaaccggtagacgttaggttggc                agccgacgttaaaacatccctgcgcatga
        actgggggccggccttgcgtgca                cgtagtcacgtagctgactttatcaatta
        ccgccgaccccgtccaagtcgcg                ctctacagtggggacattggggccacgca
                                                                            
 Sequence until next stop: 
AAAAGTCAACAACTGTAG
 K  S  Q  Q  L  * 

 Distance CDS-SECIS: 113 ; UGA-SECIS: 341

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = OMLM01014617.1:subseq_0,91592_ Strand = - Positions = 35247 - 35177
 Found by:  Infernal (score=20.37) Covels (score=15.29)
 Stem2 length = 9   Apical loop length = 12   Insertion in stem2 = 0, 0
 Free Energy = -12.4

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         (((({(((((--....([[{((({{((((((.....---.......))))))}})))}]])..--...)))))}))))
 target  GACAUAACAA--UUCAUGACAGUCACAUUUGAAAGU---CUUGUACUGAAUGAAACUUGAAUC--AUUUUGUUCUGUC
                         ****           ^^^                       ****