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

 Blastx evalue: 2e-17
 Query name: gi|755469480|gb|AHB30480.2| thioredoxin reductase 3 [Oplegnathus fasciatus]
 Query range: 59-602  (total 602)

 Target: /data/www-rg/seblastian_results/97873130/tempfiles/temptarget.fasta
 Chromosome: ML683830.1:subseq_20410135,119414_ Strand: -
 Positions:
 -Exon 1  69259        69372
 -Exon 2  68131        68247
 -Exon 3  65917        65989
 -Exon 4  63873        63992
 -Exon 5  62678        62820
 -Exon 6  60390        60505
 -Exon 7  60042        60267
 -Exon 8  59693        59785
 -Exon 9  58995        59071
 -Exon 10 55514        55670
 -Exon 11 55181        55288
 -Exon 12 51845        51940
 -Exon 13 50003        50137
 -Exon 14 49593        49658

 Redox box: no

Query   IEDGTNYQEMLLEMTGQKTVPNVFINKTHIGGCDKTLQ <---Intron---> AHKDGSLQQLLSGE---NEAYDYDLIVIGGGSGGLACSK <---In
        //|| | | /| /|/ |/||||||/| ||/|| ||| | <   1011bp   > |///||||//|       | ||||||||||||||||||| <   21
Target  LDDGPNIQRVLEDMSDQRTVPNVFVNGTHVGGYDKTFQ                AYQNGSLQRVLEDNIDGAEVYDYDLIVIGGGSGGLACSK       
        tgggcaaccgtggaagcaagcagtgagacgggtgaatc                gtcagtccagcggaagggggtgtgcagagggtggcgtta       
        taagcatagttaatgaagctcatttagcatggaaacta                caaagctagttaaatagcataaaattttgggcggtcgca       
        attccttgagaacgtcggtgctatgtaacgtatcattg                tcgtcgtgggagtcattaatttctttttttcccatatcg       
                                                                                                            

Query   tron---> EAALLGKKAMVLDYVVPTPKGTTWG <---Intron---> LGGTCVNVGCIPKKLMHQTALLGTAMQDARKFGWEFDETV <---Intro
        41bp   > ||| |||| |||||||||| ||/|| <   1924bp   > |||||||||||||||||| |||| |/||/||||||/|| | <   1052b
Target           EAATLGKKVMVLDYVVPTPLGTSWG                LGGTCVNVGCIPKKLMHQAALLGQALQDSRKFGWEYDEQV          
                 gggacgaagagcgtggcactgattg                cggatgaggtacaacaccggccgcgccgtaatgtgtggcg          
                 accctgaattttaattccctgccg                gtggcgtatggtcaattaaccttgactaacgatggaaaaa           
                 atttgaggtggatttaaatgttag                attcttatatttggaggtatgtgagatgtagatcggttga           
                                                                                                            

Query   n---> KHNWETMKMAVNNYIGSLNWGYRVALRDKNVNYVNAYAEFIEPHKIK <---Intron---> AINKRGKETFYTAAKFVLATGERPRYLGIPG
        p   > |||||||  |/ ||||||||||||/||/| | |/||||||||||||| <   2172bp   > | |//|/|||/||  ||||||||||||||||
Target        KHNWETMVEAIQNYIGSLNWGYRVSLREKTVTYLNAYAEFIEPHKIK                ATNRKGQETFHTAQTFVLATGERPRYLGIPG
              acatgaagggacatagttatgtagttagaagatcagtggtagccaaa                gaaaagcgatcagcatgcgaggaccttgacg
             taaagacttactaaatgctaggagtctgaactcatacacattacaata                ccagagaactaccactttccgagcgatgtcg
             gaccggcgagctgccagagtgtcggggaagtggcctctaattgacaag                accgaagactcaagatcaaaaagcatgtcta
                                                                                                            

Query   DKEYCITS <---Intron---> DDLFSLSYCPGKTLVIGASYVALECGGFLAGLGLDVTVMVRSILLRGFDQDMANRAGEHMEEHGVKFLRKYVPVK 
        |||||||| <   122bp    > |||||| |||||||//||||||||| |||||/||||||||||||||||||/|| ||| /|| |||||/|//||// 
Target  DKEYCITS                DDLFSLPYCPGKTLIVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQEMAERAGAYMETHGVKFIRRFVPIQ 
        gagttaaa                ggcttccttcgaacagggttggcgtggtcggagtggagagctacccgtgcgaggagggtagacggataaatgcac 
        aaaagtcg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcagcgcatacagtattggttcta 
        taacctt                ctccccgtcctcatttgtcctgtggtaattttttgtcatggcccttactcaagggaatccgattttaccgatgttg 
                                                                                                            

Query   <---Intron---> VEELEAGTPGRLKVTAKSTETDEIIEGEYNT <---Intron---> VLIAVGRDACTDKIGLDKTGVKVNPK <---Intron-
        <   256bp    > /| || | |||||| |/|||  ||/|||||| <   621bp    > ||||/||||||  |||/| |||/| | <   3324bp 
Target                 IERLEEGMPGRLKVVAQSTEGPEIVEGEYNT                VLIAIGRDACTKNIGLEKIGVKINEK            
                       agatgggacgacagggctaggcgaggggtaa                gtagagcggtaaaagtgaaggaaaga            
                       tagtaagtcggtattcaccagcattagaaac                tttctggacgcaatgtaatgtataaa            
                       tagggacgtaggggaagttaaaataaaattt                tgatttttctcacttaagttcacta             
                                                                                                            

Query   --> NGKIPVNDEEQTNVPHIYAIGDILEGKWELTPVAIQAGKLLARRLYGGSKLK <---Intron---> CDYVNVPTTVFTPLEYGACGLSEERATE
          > ||||||||||||||||/|||||||/|| |||||||||||||||||/||  /| <   225bp    > ||||||||||||||||| ||| |||| /
Target      NGKIPVNDEEQTNVPHVYAIGDILDGKLELTPVAIQAGKLLARRLFGGGFIK                CDYVNVPTTVFTPLEYGCCGLPEERAIK
            agaacgagggcaagccgtgaggatggacgcacggacggaccgcactgggtaa                tgtgagcaagtactgtgttgtcggagaa
            agatctaaaaacatcatactgattagatatcctctacgattcggttgggtta                gaatatcccttcctaaggggtcaagcta
           gtaattattgaactgttctctattgtgatatcatctgacgagtcgttttgtag                tctctaatagtttgatcttaatggacca
                                                                                                            

Query   LYGKDNIE <---Intron---> VFHSLFWPLEFTVPNRDNNKCYGKIICNKLDS <---Intron---> DRVIGFHYLGPNAGEVTQGFGAAMKCGA
         |||/||| <   3240bp   > |||/||||||/||  |||| || |||||| |/ <   1707bp   > /|||||| |||||||/|||||||/||| 
Target  EYGKENIE                VFHTLFWPLEWTVAGRDNNTCYSKIICNKHDN                NRVIGFHVLGPNAGEITQGFGAAIKCGL
        gtgagaag                gtcatttccgtagggagaaatttaaataacga                acgagtcgcgcagggaacgtgggaatgc
        aagaaata                ttacttgctagctcggaaacgacattgaaaaa                agttgtattgcacgatcagtgcctaggt
        atagacag                gtctgtgttagaatcactttccagccctatcc                ctaaattctacttgatcatttcaaatac
                                                                                                            

Query   TKEQLDSTIGIHPTCAE <---Intron---> IFTTLEVTKSSGGDITQAGCUG
        ||| |/ |||||||||| <   344bp    > /|||||/||||| |||||||||
Target  TKELLEETIGIHPTCAE                VFTTLEITKSSGKDITQAGCUG
        aagtcggaagaccatgg                gtaatgaaattgagaacggttg
        caattaactgtaccgca                ttcctatcaccgaatcacgggg
        gaaataaaacacaatag                cctagataattaatctgaccat
                                                             * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 216 ; UGA-SECIS: 219

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = ML683830.1:subseq_20410135,119414_ Strand = - Positions = 49376 - 49281
 Found by:  Infernal (score=23.55) Covels (score=24.77)
 Stem2 length = 9   Apical loop length = 18   Insertion in stem2 = 0, 0
 Free Energy = -11.56

         ..(((((((.......................(((((((((((((((................)))))))))))))))..........)))))))..
 model   uucggucaugcg----------------UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         .(({((({(((.....................{[[(((({((((((..................))))))}))))]]}......-.)))})))})).
 target  UUGCUUGGAGGUAGCACAUAUAAGUGCUUUUUUGAAGUUUUGGCUCAGAACCCCAUUCUGGGGCGAGCUACGACUGAUGACUUA-CCUUGCAAACAU
                                         ****            ^^                        ****