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

 Blastx evalue: 1e-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/590665007/tempfiles/temptarget.fasta
 Chromosome: your_sequence Strand: +
 Positions:
 -Exon 1  51412        51476
 -Exon 2  52838        53063
 -Exon 3  55087        55179
 -Exon 4  56887        56963
 -Exon 5  58585        58741
 -Exon 6  60835        60942
 -Exon 7  62308        62403
 -Exon 8  64483        64617
 -Exon 9  68430        68495

 Redox box: no

Query   IATGERPRYLGIPEDKEYRISS <---Intron---> DDLFSLPYCPGKTLVVGASYVALECAGFLVGLGLDVTVMVRSILLRGFDQDMANKIGEYMEE
        ||||||||||||| |||| ||| <   1361bp   > |||||||||||/||||||||||||||||| ||||||||||||||||||||||||/||| |/|
Target  IATGERPRYLGIPGDKEYCISS                DDLFSLPYCPGRTLVVGASYVALECAGFLAGLGLDVTVMVRSILLRGFDQDMANRIGEXMKE
        agaggccctcgacggagttaaa                ggcttccttcgaacggggttggtgtggtcggcgtggagagatactagtgcgagaaaggtaag
        tccgagcgatgtcgaaaagtgg                aattctcagcggctttgccatctagcgttcgtgtatctttgctttggtaaatcagtgaataa
        tcctaaaccgtatacgatctc                ttctctgtctagacggtatcttcggtaattactaatctaggactcaaatcgcgacattangaa
                                                                                                            

Query   HGIKFIREFVPIK <---Intron---> IEQIEEGTPGRLKVTAKSTKDDKVIEEEYNT <---Intron---> VLLAIGRDACTRKIGLDKVGVKIN
        ||/ ||||||||| <   2023bp   > /|//|||||| ||||||||  |//|| |||| <   1707bp   > |||||||| |||||||||||| ||
Target  HGVNFIREFVPIK                VERVEEGTPGILKVTAKSTTGDQIIEAEYNT                VLLAIGRDPCTRKIGLDKVGVNIN
        cggataagtgcaa                ggcggggacgacagagataaggcaagggtaa                gccgagcgctaaaagtgagggaaa
        agtattgattcta                tagtaagccgttatccacccgaattacaaac                tttctggacgcgatgtaatgtata
        taccctggtgacg                tggtgaattaagatacacaagtaatagactt                gggataatacaaattgcacagtct
                                                                                                            

Query   EK <---Intron---> TGKIPVDDMEQTNVPYIYAIGDILQDRLELTPVAIQAGRLLVQRLYAGSTIK <---Intron---> CDYVNVPTTVFTPL
        |/ <   1621bp   > ||||||/| ||||||||||/||||||/|||||||||||||||/|| ||/| | <   2093bp   > ||||||||||||||
Target  ER                TGKIPVNDEEQTNVPYIYAVGDILQDKLELTPVAIQAGRLLVRRLXAGTTTK                CDYVNVPTTVFTPL
        ga                agaacgagggcaagctatggggaccgacgcacggacggattgcactggaaaa                tgtgagcaagtact
        ag                cgatctaaaaacatcatactgattaaatatcctctacggtttggtacgccca                gaatatcccttcct
        a                agaattcttgggattgtctttatcggcggacaagacgaaggatggtntgactg                tctgttattatttg
                                                                                                            

Query   EYGACGYSGENAIQKFGEENIE <---Intron---> VYHSHFWPLEWTVPSRDNNKCYAKIICNIQDN <---Intron---> ERVIGFHVLGPNAG
        |||||||  | |//|||||||| <   1365bp   > |||||||||||||||||||||||||||| ||| <   2079bp   > ||||||||||||||
Target  EYGACGYPEETAVEKFGEENIE                VYHSHFWPLEWTVPSRDNNKCYAKIICNTQDN                ERVIGFHVLGPNAG
        gtggtgtcggagggatgggaag                gtcacttccgtagctagaaattgaaataacga                gagagtcgcgcagg
        aagcggacaacctaatgaaata                taagatgctagctccgaaaagacattgacaaa                agttgtattgcacg
        gtactgctagcaggatggactg                gccttcgagggtgacatccaccagatcttatc                gactcctcttatta
                                                                                                            

Query   EVTQGFAAAMKCGLTKEQLDSTIGIHPVCAE <---Intron---> VFTTLSITKRSGESTLQSGCUG
        |||||||||/||||||||||||/|||||||| <   3812bp   > ||||||/||||||/|  |||||
Target  EVTQGFAAAIKCGLTKEQLDSTVGIHPVCAE                VFTTLSVTKRSGENTAVSGCUG
        ggacgtgggaatgtaagccgaaggaccgtgg                gtaactgaactggaaggagttg
        atcagtccctaggtcaaatagctgtactgca                ttcctctcagcgaacctggggg
        gccagtatatatggaaaggcccaatttctag                acccgtgtgtttacttgtacag
                                                                           * 
 Sequence until next stop: 
TAA
 * 

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

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = your_sequence Strand = + Positions = 68723 - 68813
 Found by:  Infernal (score=23.15) Covels (score=22.0)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -14.58

         ..(((((((......................(((((((((((((((.................)))))))))))))))........)))))))..
 model   uucggucaugcg---------------UuaAUGAcGgccuggcccuAAAcC--cuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ...(((((((.....................([[[{(((({(((((.................)))))}))))}]]])..--.--)))))))...
 target  UGAUUAGCAGGGCAUUUAAUAAAUGCCUUCAUGAAGUCAUAGCCUGAAGCCUGCAUUGUCUGGUGGGCAGUGANGGAAGA--A--CUGCUAGCAC
                                        ****           ^^                          ****