_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       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/903793495/tempfiles/temptarget.fasta
 Chromosome: CEMB01031819.1 Strand: +
 Positions:
 -Exon 1  104883       104947
 -Exon 2  105933       106158
 -Exon 3  108252       108344
 -Exon 4  109964       110040
 -Exon 5  111617       111773
 -Exon 6  112820       112927
 -Exon 7  114838       114933
 -Exon 8  116393       116527
 -Exon 9  120894       120959

 Redox box: no

Query   IATGERPRYLGIPEDKEYRISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLVGLGLDVTVMVRSILLRGFDQDMANKIGEYMEE
        ||||||||||||| |||| |/| <   985bp    > ||||||||||||||||||||||||||||| |||||||||||||||||||||||||/| /|||
Target  IATGERPRYLGIPGDKEYCITS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQDMANKVGAHMEE
        agaggaccttgacggagttaaa                ggctttcttcgaatggggttggcgtggtcggcgtggagagctaccagtgcgagaagggcagg
        tccgagcgatgtcgaaaagtcg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgcataa
        tcaaagcctgcatacagtctc                ttttccgctcgagaggtatctactgcaatatctcataacggccccgacttgtggcaaaacgaa
                                                                                                            

Query   HGIKFIREFVPIK <---Intron---> IEQIEEGTPGRLKVTAKSTKDDKVIEEEYNT <---Intron---> VLLAIGRDACTRKIGLDKVGVKIN
        |||||||//|| | <   2093bp   > |||//||||| |/||| ||//  | /||||| <   1619bp   > |||||||||||| |||/|||||/|
Target  HGIKFIRKYVPSK                IEQVQEGTPGVLRVTAHSTENAGVFQEEYNT                VLLAIGRDACTRTIGLEKVGVKLN
        cgaataaatgcaa                agcgcggacggtcgagctagagggtcggtaa                gtcgagaggtaaaagtgagggaca
        agtattgaatcga                taataagccgttgtccaccaacgttaaaaac                tttctggacgcgctgtaatgtata
        tgcgctaatcccg                tagtgaattccaacatttaattgatgaacta                ggataagtccaagtcggataggct
                                                                                                            

Query   EK <---Intron---> TGKIPVDDMEQTNVPYIYAIGDILQDRLELTPVAIQAGRLLVQRLYAGSTIK <---Intron---> CDYVNVPTTVFTPL
        || <   1576bp   > ||||||/|/|||||||||||||/|/ /|||||||||||||| /||| |/  | <   1046bp   > ||||||||||||||
Target  EK                TGKIPVNDVEQTNVPYIYAIGDVLEGKLELTPVAIQAGRLLARRLYGGAKTK                CDYVNVPTTVFTPL
        ga                agaacgagggcaagctatgagggtggacgcacggacggatcgcactgggaaa                tgtgagcaagtacc
        aa                cgatctaataacatcatactgattagatatcctctacggttcggtaggcaca                gaatatcccttcct
        a                aagactcttggaatgttctctattgacaagcaagatggtaggtgggtcaaaag                tctgcttcaacttg
                                                                                                            

Query   EYGACGYSGENAIQKFGEENIE <---Intron---> VYHSHFWPLEWTVPSRDNNKCYAKIICNIQDN <---Intron---> ERVIGFHVLGPNAG
        |||||||| | ||/ ||/ ||| <   1910bp   > ||||/|||||||||||||||||||||| | |  <   1459bp   > ||||||||||||||
Target  EYGACGYSEEKAIEIFGDRNIE                VYHSYFWPLEWTVPSRDNNKCYAKIICCIPDK                ERVIGFHVLGPNAG
        gtggtgttggagagatggaaag                gtcatttccgtagctcgaaattgaaattacga                gcgagtcgcgcagg
        aagcggacaaactattgagata                taagatgctagctccgaaaagacattggtcaa                agttgtattgcacg
        attcttctaaaaagatgcattg                ttctccgggagtcacgtctactagatcctctg                gtcttctggtatta
                                                                                                            

Query   EVTQGFAAAMKCGLTKEQLDSTIGIHPVCAE <---Intron---> VFTTLSITKRSGESTLQSGCUG
        |/|||||||/|||/||| ||||||||||||| <   4366bp   > /|||||/|||||   |||||||
Target  EITQGFAAAIKCGITKELLDSTIGIHPVCAE                IFTTLSVTKRSGGDILQSGCUG
        gaacgtgggaatgaaagccgaaagaccgtgg                ataattgaactgggacctgttg
        atcagtccctaggtcaattagctgtactgca                ttcctctcagcggattacgggg
        atagctaacagcacaaaaactaagttactag                accagtgagcatatcgatacat
                                                                           * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 258 ; UGA-SECIS: 261

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CEMB01031819.1 Strand = + Positions = 121218 - 121295
 Found by:  Infernal (score=27.88) Covels (score=32.08)
 Stem2 length = 9   Apical loop length = 19   Insertion in stem2 = 0, 0
 Free Energy = -13.23

         ..(((((((.......(((((((((((((((.................)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         .....((((---....([[[((((({((((...................))))})))))]]])......-...)))).....
 target  GAAGAUGCU---UCUAUGAAGUUGCAGCCUUAAACCAGGAUUUUCUGGUAGGCAGCAAUGGAAGAAUUG-CUUGGCACAGCU
                         ****           ^^^                         ****