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

 Blastx evalue: 4e-25
 Query name: gi|1041125537|ref|XP_017286897.1| PREDICTED: thioredoxin-like protein AAED1 [Kryptolebias marmoratus]
 Query range: 1-298  (total 303)

 Target: /data/www-rg/seblastian_results/309988870/tempfiles/temptarget.fasta
 Chromosome: WARS01000046.1:subseq_159331,200000_:subseq_0,120000_ Strand: +
 Positions:
 -Exon 1  95809        95914
 -Exon 2  96730        96808
 -Exon 3  96952        97005
 -Exon 4  97188        97233
 -Exon 5  98057        98184
 -Exon 6  98286        98400
 -Exon 7  99373        99495
 -Exon 8  99997        100134
 -Exon 9  100972       101076

 Redox box: YES

Query   MADGVAVSEETLTNSLNLFVNLSNVLLQSAKQDAAA <---Intron---> SLETFVPHKITTLFGLITAGANFYKS <---Intron---> IGVKTK
        ||/ |||||||/|/ | | |//| |||/ |||/|   <   815bp    > |||/||||||||||||||||| |||| <   143bp    > /||| |
Target  MAEDVAVSEETVTSGLTLLVDVSKVLLEKAKQEAED                SLESFVPHKITTLFGLITAGAQFYKS                LGVKKK
        aggggggtggagaagcaccgggaagccgagacgggg                tcgatgccaaaactgcaagggcttaa                cggaaa
        tcaatctcaactcggtctttatgatttaacaaaca                actagttcaatccttgttccgcataag                tgtaaa
        gtgcgcggggcaattgtggccgcgcccgacggaaa                ccggttcgtacctgccgcgcaggcca                ctagggg
                                                                                                            

Query   SEAEAVWKKFYH <---Intron---> HEAVREQVEELLQLE <---Intron---> DEWDSFLQSVDEGLLTADEQLPGGKMADGLNPDCLFTDARS
        ||||| |/|||| <   182bp    > | ||||||||||||| <   823bp    >  |||/||/|||||| | | || |||/|| |/|/  ||| ||
Target  SEAEATWQKFYH                HAAVREQVEELLQLE                GEWDAFLESVDEGLQTTDGQLRGGKVADSLSPEAAFTDGRS
        aggggatcattc                cgggagcgggccccg                ggtggtcgaggggccaaggcccggagggacacgggtaggca
        gacaccgaataa                acctgaataattata                gagacttagtaagtaccagatgggatcagtgcacctcaggg
        taagccgggtt                ccgagaggaggtgggg                cggcccggtgcgttgcgcgggtaaaggccgccgtgctcact
                                                                                                            

Query   GK <---Intron---> SVTLGHFLGQGQKLLLVLIRHFGULPURDHVAELEASR <---Intron---> DLLEARSVQVLVVSFGGVEGAQLWLEQT
        || <   101bp    > |||||||| || |||||||||||||||||||||||||| <   972bp    >   |/|||||||||||||||||/||||||
Target  GK                SVTLGHFLDQGPKLLLVLIRHFGULPURDHVAELEASR                ADLKARSVQVLVVSFGGVEGARLWLEQT
        ga                agacgctcgcgcacccgcacctgtcctcgcgggcggac                ggcagctgcgtggttggggggactcgca
        ga                gtctgattaagcattttttgatggtcggaatcatacgg                catacgctattttctggtagcgtgtaac
        g                gcgtgtccgtgtgggggtccatcaaggaaccgcgggccg                tccgtggggcggcccccggacggggggt
                                                 *  *                                                       

Query   GCTFEMLLDPQRK <---Intron---> VYRSFGLGASYAKVMKFSCLLHYSEYRTANIDFPDFPPRLLEDLYQ <---Intron---> MGGDFLLDD
        ||||///|||/|| <   501bp    >  |||||||/||||||/| ||| ||||   / |||| || ||||/|| <   837bp    > |||||||||
Target  GCTFDIVLDPERK                TYRSFGLGSSYAKVMRFGCLLQYSEYGAVDRDFPDVPPHLLEDIYQ                MGGDFLLDD
        gtatgagcgcgaa                atcatgcgtttgagaatgtcccttgtggggagtcggcccccggatc                agggttcgg
        ggctatttacaga                caggtgtgccacattgtggttaacaagctagatcatccattaataa                tggatttaa
        atccccggtaggg                gcccccccgcccggggcccgggcggcgtgcaccgccgtcggacccg                gatctggcc
                                                                                                            

Query   SGKVLLSHPSKSPLDRPGLTDVLQAA
        /|||||||| |/||||| / |/||||
Target  AGKVLLSHPCKTPLDRPTVKDILQAA
        ggagcctcctaaccgacagagaccgg
        cgatttcacgacctagcctaattacc
        agggtcccgtactgcgggggccggct
                                  
 Sequence until next stop: 
GACCCAACGACGCCGTGA
 D  P  T  T  P  * 

 Distance CDS-SECIS: 93 ; UGA-SECIS: 492

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = WARS01000046.1:subseq_159331,200000_:subseq_0,120000_ Strand = + Positions = 101170 - 101255
 Found by:  Infernal (score=26.95) Covels (score=29.48)
 Stem2 length = 10   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -21.12

         ..(((((((.........(((((((((((((((.................))))))))))))))).............)))))))..
 model   uucggucaugcg--UuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuu----u-uuucaugaccggc
         .(((((([((........{[[(((((((((((...................)))))))))))]]}.........-..))])))))).
 target  CUCUUUGAUUCACGUUUAUGAGGUCACGUCUCGCACUCGUGGCGCCAUGAAGAGGCGUGACUGAUGCCGAACUG-UAAAGCAAAGAC
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