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

 Blastx evalue: 4e-32
 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/650146929/tempfiles/temptarget.fasta
 Chromosome: JXSJ01000123.1:subseq_305390,55111_ Strand: -
 Positions:
 -Exon 1  52388        52457
 -Exon 2  51937        52113
 -Exon 3  51457        51555
 -Exon 4  51260        51352
 -Exon 5  51020        51176
 -Exon 6  50650        50765
 -Exon 7  50459        50536
 -Exon 8  50186        50325
 -Exon 9  50006        50095

 Redox box: no

Query   MMASALANRAIGAIVGSAVADAAA <---Intron---> QPLHWVYDLQKLKGILALNPNPEFHPESANPFYRRETGKQSCYGDQAYVLLESLSECGG 
         ||/|||/|||||||||||||||| <   274bp    > ||| || || || |/|/ /|||||  || ||||||/ ||||||||||/||||||||||| 
Target  QMAAALADRAIGAIVGSAVADAAA                QPLTWVCDLPKLHGVLSQHPNPEFCSESFNPFYRRQMGKQSCYGDQAFVLLESLSECGG 
        cagggcggagaggaggtggggggg                cccatgtgccaccggctcccacgtttgttacttaacagacattggcgtgccgtttgtgg 
        atccctcagctgcttgcctcacc                cactcgtgatcatagttcaacacatgcactactaggatgaaggagaacttttactcagg  
        ggtatgccagaaccaaattataa                agcgcggcccgggtgtgtgcactgcctaacctccggggcggcccgcggtcggacgtata  
                                                                                                            

Query   <---Intron---> LNVDDLKQRTLKVFGPGSEYDTPVNDPYRERGG <---Intron---> PRPQLPIDGPWRHASLKSFLKNVDAGKEETG <---
        <   381bp    > |||||||||||| ||||||||||||||||/||| <   104bp    > |||||||/||||||||||||||||||||||| <   
Target                 LNVDDLKQRTLKFFGPGSEYDTPVNDPYRDRGG                PRPQLPIEGPWRHASLKSFLKNVDAGKEETG     
                       cagggcaccacattgcgtgtgacgagctagagg                caccccaggctacgataatcaaggggaggag     
                      gtataataagctattgcgcaaacctaacagagg                gcgcatctagcggacgtagttaatacgaaac      
                      gattctgggcaggctctaagtcgtctttcacaa                gaatggctaaagatatggccggtgtacagga      
                                                                                                            

Query   Intron---> CENDCQIDGIAKLAPIVAFYAGQPDMLEKVEQAIRVTQNNDECVAETLAAAR <---Intron---> FLEHFILNGPDPKALDAVLNQ
         83bp    > ||||||||||||||||||||||/||||||||||/|||||||||||||||||| <   254bp    > |||/||||||||||||/|| |
Target             CENDCQIDGIAKLAPIVAFYAGKPDMLEKVEQAVRVTQNNDECVAETLAAAR                FLEYFILNGPDPKALDSVLAQ
                   tgagtcaggagacgcaggttggacgacgaggcggcgacaaggtgggacggga                tcgttacagcgcagtgtgcgc
                  ggaaagatagtcatccttctacgacattaataactgtcaaaaagtcactcccg                ttaatttagcacactacttca
                  ctgcctgttaatagttagtttaagtcggaagggactccgcttatgagtgata                gcggtccgttttaacgcagctg
                                                                                                            

Query   LNDPNRKQPQDLDKAVIG <---Intron---> HIHQVKENLSKTPQKLIPSVFTNAUG <---Intron---> LPGAFQAALHGVLTATRYETAVKD
        |||| ||||||||||||| <   113bp    > |||||||||||||//|||/|| |||| <   133bp    > ||||||||||||||| /|| |//|
Target  LNDPKRKQPQDLDKAVIG                HIHQVKENLSKTPKELIPTVFPNAUG                LPGAFQAALHGVLTAKQYEQAIRD
        cagcaaacccgcgaggag                caccgagattaacagcacagtcagtg                tcggtcggccggcagactgcgaag
        taacagaacaataactt                gataataaatcaccaattccttcacg                gtcgctacctagttccaaaaactga
        ctcagaggtgtgcaact                gcttggggtaagttggatctgtataa                tgatgcaaggtacgatgatggttac
                                                                  *                                         

Query   TMSCGGCTCSRGSFIGACLGAQ <---Intron---> VGLEGIPESWKSKTLQYDLVLEHAKKITKH
         ||||||||||||||||||||| <    90bp    > /| |||| ||/|||| || |||||||||||
Target  NMSCGGCTCSRGSFIGACLGAQ                IGFEGIPASWRSKTLCYDAVLEHAKKITKH
        aaatggtataagttaggtcggc                agtggacgttataacttgggtgcgaaaaac
        atgggggcggggcttgcgtgca                tgtagtcccggcactgaacttaacaatcaa
        cgctaacctcagcctacttgtg                tatgatatcgacatgttcagggtcggacac
                                                                            
 Sequence until next stop: 
CACCAGTAG
 H  Q  * 

 Distance CDS-SECIS: 66 ; UGA-SECIS: 297

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JXSJ01000123.1:subseq_305390,55111_ Strand = - Positions = 49939 - 49873
 Found by:  Infernal (score=30.82) Covels (score=23.18)
 Stem2 length = 10   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -16.02

         ..(((((((.......(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...({((((---....([[{((((((((((..........-----...))))))))))}]])..--.--.))))})...
 target  ACAGAACAG---UUAAUGAAGGUUCUUGUCUAAACUAUUG-----GAUGGCAAGAGCCAGAAGU--C--UUUGUCUCUG
                         ****           ^^^                        ****