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

 Blastx evalue: 2e-20
 Query name: gi|844287339|gb|AKN04699.1| thioredoxin reductase 1, partial [Meleagris gallopavo]
 Query range: 1-341  (total 341)

 Target: /data/www-rg/seblastian_results/906219829/tempfiles/temptarget.fasta
 Chromosome: ULFQ01000007.1:subseq_14657493,135492_ Strand: -
 Positions:
 -Exon 1  64509        64573
 -Exon 2  61991        62216
 -Exon 3  60184        60276
 -Exon 4  59065        59141
 -Exon 5  58237        58393
 -Exon 6  57748        57855
 -Exon 7  56141        56236
 -Exon 8  54136        54270
 -Exon 9  50000        50065

 Redox box: no

Query   IATGERPRYLGIPEDKEYRISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLVGLGLDVTVMVRSILLRGFDQDMANKIGEYMEE
        |||||||||| || |||| |/| <   2292bp   > ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||/|||
Target  IATGERPRYLNIPGDKEYCITS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQDMANKIGEHMEE
        agaggacctcaacggagttaaa                ggcttccttcgaatggggttggcgtggtcggcgtggagagctaccagtgcgagaaaggcagg
        tccgagcgatatcgaaaagtcg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgaataa
        tctaaatctcctaacaatccc                ttcccagtccaaaaggtattctttataatttgttatgtcggtctcggcttgtgataaagtgag
                                                                                                            

Query   HGIKFIREFVPIK <---Intron---> IEQIEEGTPGRLKVTAKSTKDDKVIEEEYNT <---Intron---> VLLAIGRDACTRKIGLDKVGVKIN
        ||/||||//|| | <   1714bp   > ||||//|||| |||||//|// //|| |||| <   1042bp   > |/|||||||||/|||| ||||/||
Target  HGVKFIRKYVPTK                IEQIKKGTPGLLKVTAQATENSEIIEGEYNT                VMLAIGRDACTKKIGLQKVGVRIN
        cggataaatgcaa                agcaaagacgtcagagcgagatgaagggtaa                gacgagaggtaaaagccagggaaa
        agtattgaatcca                taataagccgttatccaccaacattagaaac                tttctggacgcaatgtaatgtgta
        ttagcaaatgcag                tagtgaattaaaatatgtagctaataaacca                ggaaaaatccaaatcagataggct
                                                                                                            

Query   EK <---Intron---> TGKIPVDDMEQTNVPYIYAIGDILQDRLELTPVAIQAGRLLVQRLYAGSTIK <---Intron---> CDYVNVPTTVFTPL
        |  <   671bp    > ||||||/| |||||||||||||/|/ / ||||||||||||||/||| |/  | <   381bp    > |||/||||||||||
Target  EN                TGKIPVNDKEQTNVPYIYAIGDVLEGKPELTPVAIQAGRLLVRRLYDGAFTK                CDYINVPTTVFTPL
        ga                agaacgagagcaagctatgagggcggacgcacggacggattgaactgggtaa                tgtaagcaagtact
        aa                cgatctaaaaacatcatactgattagacatcctctacggtttggtaagctca                gaatatcccttcct
        a                taaactttcgaaacgtcctttatcggcaaacccgatggaggggggtttaacag                tttaccctaacatg
                                                                                                            

Query   EYGACGYSGENAIQKFGEENIE <---Intron---> VYHSHFWPLEWTVPSRDNNKCYAKIICNIQDN <---Intron---> ERVIGFHVLGPNAG
        |||||||| | ||//||   || <   1511bp   > ||||/||||||||||||||/||||||||/ |  <   1870bp   >  |||||||||||||
Target  EYGACGYSEEKAIERFGNNRIE                VYHSYFWPLEWTVPSRDNNRCYAKIICNLADR                NRVIGFHVLGPNAG
        gtggtgttggagagatgaaaag                gtcatttccgtagctcgaaattgaaatacgga                acgagtcgcgcagg
        aagcggacaaactagtgaagta                taagatgctagctccgaaaggacattgatcag                agttgtattgcacg
        atactttaaaaataatcttgtg                tcctccgagggacacgcccactaattcttatg                tatttctgttctta
                                                                                                            

Query   EVTQGFAAAMKCGLTKEQLDSTIGIHPVCAE <---Intron---> VFTTLSITKRSGESTLQSGCUG
        |/|||||||/|||/ |||||||||||||||| <   4070bp   > /|||||/||||| /  ||||||
Target  EITQGFAAAIKCGIRKEQLDSTIGIHPVCAE                IFTTLSVTKRSGGNVAQSGCUG
        gaacgtgggaatgaaagctgaaagaccgtgg                ataactgaactggaggctgttg
        atcagtccctaggtgaaatagctgtactgca                ttcctctcagcggatcacgggg
        atagataaccataagaaagccaaactactgg                actagggagcttatttgtacat
                                                                           * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 227 ; UGA-SECIS: 230

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = ULFQ01000007.1:subseq_14657493,135492_ Strand = - Positions = 49772 - 49696
 Found by:  Infernal (score=33.86) Covels (score=32.23)
 Stem2 length = 10   Apical loop length = 16   Insertion in stem2 = 0, 0
 Free Energy = -18.41

         ..(((((((..........(((((((((((((((................)))))))))))))))........)))))))..
 model   uucggucaugcg---UuaAUGAcGgccuggcccuAAAcC-cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((..........([[[((((({(((((................)))))})))))]]])----..-.)))))))..
 target  CAUUGGCAAGAUGCUUCCAUGAAGUCGUAGCCUAAAACCAGUUUCUCUGGUAGGCAACGAUGGAA----CA-AUUGCCAGCA
                            ****           ^^^                        ****