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

 Blastx evalue: 3e-79
 Query name: gi|908520312|ref|XP_013120966.1| PREDICTED: crystallin J1A-like isoform X1 [Oreochromis niloticus]
 Query range: 1-339  (total 343)

 Target: /data/www-rg/seblastian_results/37117216/tempfiles/temptarget.fasta
 Chromosome: JACSYO010000511.1:subseq_748545,100000_ Strand: -
 Positions:
 -Exon 1  52254        52323
 -Exon 2  51771        51947
 -Exon 3  51575        51673
 -Exon 4  51400        51492
 -Exon 5  51157        51313
 -Exon 6  50735        50850
 -Exon 7  50468        50545
 -Exon 8  50194        50333
 -Exon 9  50009        50095

 Redox box: no

Query   MMASALANRAIGAIVGSAVADAAA <---Intron---> QPLHWVYDLQKLKGILALNPNPEFHPESANPFYRRETGKQSCYGDQAYVLLESLSECGG 
         ||///|||||||||||||||||| <   306bp    > ||||||||||||/|||| /| ||| ||| ||||||/||/|||||||| ||||||| ||| 
Target  QMAASVANRAIGAIVGSAVADAAA                QPLHWVYDLQKLQGILAQHPEPEFCPESFNPFYRRQTGQQSCYGDQAVVLLESLSACGG 
        caggtggaagaggaggtggggggg                cccctgtgccaccgacgcccgcgttcgttacttaacagccattggcgggtcgtctgtgg 
        atccctcagctgcttgcctcacc                cactagtaataatagttcaacacatgcactactaggacgaaggagaacttttactccgg  
        agtatgccaaaaccaaaatgtaa                ggcccggtccgggggtgtgtaacgcccggcctccggggcggcccgcgcccgggcgtgtg  
                                                                                                            

Query   <---Intron---> LNVDDLKQRTLKVFGPGSEYDTPVNDPYRERGG <---Intron---> PRPQLPIDGPWRHASLKSFLKNVDAGKEETG <---
        <    97bp    > |||||||||||| ||||||||||/||||||||| <    82bp    > |||||||/||||||||||||||||||||||| <   
Target                 LNVDDLKQRTLKFFGPGSEYDTPINDPYRERGG                PRPQLPIEGPWRHASLKSFLKNVDAGKEETG     
                       cagggcaccacattgcgtgtgacaagctagagg                caccccaggctacgataatcaaggggaggag     
                      gtataataagctattgcgcaaacctaacagagg                gcgcatctagcggacgtagttaatacgaaac      
                      tattctggggtgactttaagtcgtccctcagaa                gaatggccgcggacatggccggtgtgcaggg      
                                                                                                            

Query   Intron---> CENDCQIDGIAKLAPIVAFYAGQPDMLEKVEQAIRVTQNNDECVAETLAAAR <---Intron---> FLEHFILNGPDPKALDAVLNQ
         86bp    > |||||||||||||||/||||||/||||||||||/||||| | |||||||||| <   306bp    > |||||||||||||||||||/|
Target             CENDCQIDGIAKLAPLVAFYAGKPDMLEKVEQAVRVTQNYDACVAETLAAAR                FLEHFILNGPDPKALDAVLDQ
                   tgagtcaggagacgccggttggacgacgaggcggcgacatggtgggacggga                tcgctacagcgcagcgggcgc
                  ggaaagatagtcatccttctacgacattaataactgtcaaaacgtcactcccg                ttaatttagcacactacttaa
                  ctgcctgctaccagttggtttgagtcggaatggaccccgcttatgagcaata                gcggtccgctttcacgcggccg
                                                                                                            

Query   LNDPNRKQPQDLDKAVIG <---Intron---> HIHQVKENLSKTPQKLIPSVFTNAUG <---Intron---> LPGAFQAALHGVLTATRYETAVKD
        |/|||||||||||/|/|| <   189bp    > ||||||||||||||/|||/|| | || <   134bp    > |||||||||||||||  || ||/|
Target  LSDPNRKQPQDLDRAIIG                HIHQVKENLSKTPQELIPAVFPNTUG                LPGAFQAALHGVLTAKHYEQAVRD
        cagcaaacccgcgagaag                caccgagactaaccgcacggtcaatg                tcggtcggccggcagactgcggag
        tgacagaacaatagctt                gataataaatcaccaattccttcacg                gtcgctacctagttccaaaaactga
        ctcgcaggcgtgcacct                gcttggggtaggttgggcttgtacaa                tgctgcaagatacggcgctggtcac
                                                                  *                                         

Query   TMSCGGCTCSRGSFIGACLGAQ <---Intron---> VGLEGIPESWKSKTLQYDLVLEHAKKITK
        |||||||||||||||||||||| <    98bp    > /| |||| |||||| /|/ ||||||||||
Target  TMSCGGCTCSRGSFIGACLGAQ                IGSEGIPASWKSKTQRYESVLEHAKKITK
        aaatggtatacgttaggtcggc                agtggacgttataacctgtgtgcgaaaaa
        ctgggggcggggcttgcgtgca                tgcagtcccgacacagaacttaacaatca
        cgccgacctcagcccacttgcg                tatgatatcgacacgctgggggtcggaca
                                                                           
 Sequence until next stop: 
CAACACCAATAG
 Q  H  Q  * 

 Distance CDS-SECIS: 75 ; UGA-SECIS: 303

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JACSYO010000511.1:subseq_748545,100000_ Strand = - Positions = 49933 - 49860
 Found by:  Infernal (score=35.32) Covels (score=23.91)
 Stem2 length = 10   Apical loop length = 13   Insertion in stem2 = 0, 0
 Free Energy = -19.78

         ..(((((((.......(((((((((((((((................))))))))))))))).........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuu-uuucaugaccggc
         ((({(((((.......{[[{((((((((((..........-----...))))))))))}]]}.....-...)))))})))
 target  UUAACAGAACAGUGAAUGAAGGUUCUUGCCCAAACUGUUG-----GACGGCAGGAGCCAGAUGUUUU-UGUUUCUGAUGA
                         ****           ^^^                        ****