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

 Blastx evalue: 3e-21
 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/117840987/tempfiles/temptarget.fasta
 Chromosome: CM003714.1:subseq_52366872,114789_ Strand: -
 Positions:
 -Exon 1  63301        63365
 -Exon 2  61699        61924
 -Exon 3  59509        59601
 -Exon 4  57734        57810
 -Exon 5  55947        56103
 -Exon 6  53744        53851
 -Exon 7  52296        52391
 -Exon 8  50000        50134
 -Exon 9  46818        46883

 Redox box: no

Query   IATGERPRYLGIPEDKEYRISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLVGLGLDVTVMVRSILLRGFDQDMANKIGEYMEE
        ||||||||||||| |||| ||| <   1376bp   > ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||/|
Target  IATGERPRYLGIPGDKEYCISS                DDLFSLPYCPGKTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQDMANKIGEYMKE
        agaggccctcgacggagttaaa                ggcttccttcgaacggggttggtgtggtcggcgtggagagatactagtgcgagaaaggtaag
        tccgagcgatgtcgaaaagtgg                aattctcagcgactttgccatctagcgttcgtgtatctttgctttggtaaatcaatgaataa
        tcttgaaccgtagacaatctc                ttctctgtctaggcggtattttcggtaattaataatctaggacccaaatcgcgacattatgaa
                                                                                                            

Query   HGIKFIREFVPIK <---Intron---> IEQIEEGTPGRLKVTAKSTKDDKVIEEEYNT <---Intron---> VLLAIGRDACTRKIGLDKVGVKIN
        ||| ||||||||| <   2097bp   > |||/|/|||| ||||||||  //|/| |||| <   1698bp   > |||||||| ||||||||||||/||
Target  HGINFIREFVPIK                IEQVEDGTPGVLKVTAKSTTGNQVMEGEYNT                VLLAIGRDPCTRKIGLDKVGVRIN
        cgaatacgtgcaa                agcggggacggcagagataagacgagggtaa                gtcgagcgctaaaagtgagggcaa
        agtattgattcta                taataagccgttatccacccgaattagaaac                tttctggacgcgatgtaatgtgta
        taccttgatgacg                tagtgtattacgatacgtaggcaagagactt                gggataatacaaattgcacagtct
                                                                                                            

Query   EK <---Intron---> TGKIPVDDMEQTNVPYIYAIGDILQDRLELTPVAIQAGRLLVQRLYAGSTIK <---Intron---> CDYVNVPTTVFTPL
        || <   1630bp   > ||||||/| |||||||||||||||||/|||||||||||||||/|||||/| | <   2095bp   > ||||||||||||||
Target  EK                TGKIPVNDEEQTNVPYIYAIGDILQDKLELTPVAIQAGRLLVRRLYAGATTK                CDYVNVPTTVFTPL
        ga                agaacgagggcaagctatgaggaccgacgcacggacggattgcactgggaaa                tgtgagcaagtact
        aa                cgatctaaaaacatcatactgattaaatatcctctacggtttggtacgccca                gaatatcccttcct
        a                agaattcctgggatgatctttatcggcggacaagacgtaggatggtttgactg                tctgttattatttg
                                                                                                            

Query   EYGACGYSGENAIQKFGEENIE <---Intron---> VYHSHFWPLEWTVPSRDNNKCYAKIICNIQDN <---Intron---> ERVIGFHVLGPNAG
        |||||||| | |//|||||||| <   1352bp   > |||||||||||||||||||||||||||||||| <   2161bp   > |||||||||||/||
Target  EYGACGYSEETAVEKFGEENIE                VYHSHFWPLEWTVPSRDNNKCYAKIICNIQDN                ERVIGFHVLGPHAG
        gtggtgttggagggatgggaag                gtcacttccgtagctagaaattgaaataacga                gagagtcgcgccgg
        aagcggacaacctaatgaaata                taagatgctagctccgaaaagacattgataaa                agttgtattgcacg
        gtactgctagcaggatagactg                gctttcgagggtgacatccactagatcttatt                gaattctcttatta
                                                                                                            

Query   EVTQGFAAAMKCGLTKEQLDSTIGIHPVCAE <---Intron---> VFTTLSITKRSGESTLQSGCUG
        |||||||/||||||||||||||||||||||| <   3116bp   > ||||||/||||||/|  |||||
Target  EVTQGFASAMKCGLTKEQLDSTIGIHPVCAE                VFTTLSVTKRSGENTTVSGCUG
        ggacgtgtgaatgtaagccgaaagaccgtgg                gtaactgaactggaaagagttg
        atcagtccctaggtcaaatagctgtactgca                ttcctctcagcgaacctggggg
        accagtattgattgaaaggcccaatttctag                acccgtgtgtttacatgtacat
                                                                           * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 249 ; UGA-SECIS: 252

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = CM003714.1:subseq_52366872,114789_ Strand = - Positions = 46568 - 46492
 Found by:  Infernal (score=29.69) Covels (score=26.95)
 Stem2 length = 10   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -12.63

         ..(((((((.......(((((((((((((((.................)))))))))))))))..........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuu-u-uuucaugaccggc
         .....((((---....([[[((((({(((((.................)))))})))))]]])......-.-.)))).....
 target  AUGAAUGCU---UUCAUGAAGUCAUAGCCUGAAGCCUGCAUUGUCUGGUGGGCAGUGAUGGAAGAACUG-C-UAGCACAGCU
                         ****           ^^                          ****