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

 Blastx evalue: 9e-54
 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/111983627/tempfiles/temptarget.fasta
 Chromosome: JXSJ01000123.1:subseq_358337,55376_ Strand: -
 Positions:
 -Exon 1  5669         5738
 -Exon 2  5202         5378
 -Exon 3  4848         4946
 -Exon 4  4662         4754
 -Exon 5  4422         4578
 -Exon 6  3844         3959
 -Exon 7  3505         3582
 -Exon 8  3186         3325
 -Exon 9  3006         3095

 Redox box: no

Query   MMASALANRAIGAIVGSAVADAAA <---Intron---> QPLHWVYDLQKLKGILALNPNPEFHPESANPFYRRETGKQSCYGDQAYVLLESLSECGG 
         ||/|||/|||||||||||||||| <   290bp    > ||| || || || |/|/ /|||||| || ||/||||||||||/||||/||||||||||| 
Target  QMAAALADRAIGAIVGSAVADAAA                QPLTWVCDLPKLHGVLSQHPNPEFHFESINPYYRRETGKQSCFGDQAFVLLESLSECGG 
        cagggcggagaggaggtggggggg                cccatgtgccaccggctcccacgtctgtaacttaagagacattggcgtgccgtttgtgg 
        atccctcagctgcttgcctcacc                cactcgtgatcatagttcaacacatatactacaaggacgaaggtgaacttttactcagg  
        ggtatgccagaaccaaattataa                agcgcggcccgggtgtgtgcactgcttgacccccggggcagcctacgatcgggcgtata  
                                                                                                            

Query   <---Intron---> LNVDDLKQRTLKVFGPGSEYDTPVNDPYRERGG <---Intron---> PRPQLPIDGPWRHASLKSFLKNVDAGKEETG <---
        <   255bp    > |||||||||||| ||||||||||||||||//|| <    93bp    > | |||||/||||||||||||||||||||||| <   
Target                 LNVDDLKQRTLKFFGPGSEYDTPVNDPYRDKGG                PTPQLPIEGPWRHASLKSFLKNVDAGKEETG     
                       cagggcaccacattgcgtgtgacgagctagagg                caccccaggctacgataatcaaggggaggag     
                      gtataataagctattgcgcaaacctaacagaag                gcccatctagcggacgtagttaatacgaaac      
                      gattttgggcaggctctaagtcatctttcacaa                gaatggctaaagatatggccggtgtacagga      
                                                                                                            

Query   Intron---> CENDCQIDGIAKLAPIVAFYAGQPDMLEKVEQAIRVTQNNDECVAETLAAAR <---Intron---> FLEHFILNGPDPKALDAVLNQ
         83bp    > ||||||||||||||||||||||/||||||/|||/|||||||||||||||||| <   462bp    > |||/||||||||||||/|| |
Target             CENDCQIDGIAKLAPIVAFYAGKPDMLEKMEQAVRVTQNNDECVAETLAAAR                FLEYFILNGPDPKALDSVLAQ
                   tgagtcaggagacgcaggttggacgacgaagcggcgacaaggtgggacggga                tcgttacagcgcagtgtgcgc
                  ggaaagatagtcatccttctacgacattaataactgtcaaaaagtcactcccg                ttaatttagcacactacttca
                  ctgcctgttaatagttagtttaagtcggaagggactccgcttatgagtgata                gcggttcgttttaacgcagctg
                                                                                                            

Query   LNDPNRKQPQDLDKAVIG <---Intron---> HIHQVKENLSKTPQKLIPSVFTNAUG <---Intron---> LPGAFQAALHGVLTATRYETAVKD
        |||| ||||||||||||| <   261bp    > ||||||||||||||/|||/||/|/|| <   179bp    > ||||||||||||||| /|| |//|
Target  LNDPKRKQPQDLDKAVIG                HIHQVKENLSKTPQELIPTVFSNSUG                LPGAFQAALHGVLTAKQYEQAIRD
        cagcaaacccgcgaggag                caccgagattaaccgcacagttattg                tcggtcggccggcagactgcgaag
        taacagaacaataactt                gataataaatcaccaattccttcacg                gtcgctacctagttccaaaaactga
        ctcagaggtgtgcaact                gcttggggtaagttggacctatacca                tgatgcaaggtacgatgatggttac
                                                                  *                                         

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

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

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JXSJ01000123.1:subseq_358337,55376_ Strand = - Positions = 2939 - 2873
 Found by:  Infernal (score=31.08) Covels (score=22.98)
 Stem2 length = 10   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -16.02

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