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

 Blastx evalue: 4e-16
 Query name: gi|844287341|gb|AKN04700.1| thioredoxin reductase 2, partial [Meleagris gallopavo]
 Query range: 3-450  (total 450)

 Target: /data/www-rg/seblastian_results/994922032/tempfiles/temptarget.fasta
 Chromosome: WARS01000015.1:subseq_17447025,200000_:subseq_0,120000_ Strand: +
 Positions:
 -Exon 1  92886        93031
 -Exon 2  93384        93459
 -Exon 3  95415        95480
 -Exon 4  95794        95864
 -Exon 5  99987        100095
 -Exon 6  100192       100366
 -Exon 7  105859       105995
 -Exon 8  107459       107554
 -Exon 9  107985       108077
 -Exon 10 109329       109400
 -Exon 11 109764       109861
 -Exon 12 110469       110595

 Redox box: no

Query   GTKWGLGGTCVNVGCIPKKLMHQAALLGGALKDAQHYGWSMAHPVHHSW <---Intron---> SVMAQAVQNYVKSLNWGHRVQLQDK <---Intro
        |||||||||||||||||||||||||||| |/|||| ||| // |/ | | <   352bp    > / ||/||||/|/||||||||||||| <   1955b
Target  GTKWGLGGTCVNVGCIPKKLMHQAALLGTAVKDAQKYGWQISGPICHDW                ATMAEAVQNHVRSLNWGHRVQLQDK          
        gaatgcggatgaggtacaacaccggccgaggaggcatgtcatgcatcgt                gaaggggcacgatcatgcagcccga          
        gcaggtggcgtatggtcaattaaccttgcctaacaaaggatcgctgaag                cctcactaaatgctaggagtataaa          
        tcggtttcgttttccttgaggcgatatctacattggccggctgacccc                gccgagctacccgtgcgtcatgggcg          
                                                                                                            

Query   n---> KVKYFNMKGSFLDSHTVCGLAKGGKKTTLTAEKIVIATGGRPKYPTH <---Intron---> ITGALEYGITSDDLFWLKDSPGKT <---In
        p   >                          /| |||/ ||/||||||/|||/ <   313bp    > |/|| |/||||||/|||| ||||| <   41
Target        -------------------------QTILTAKNIVVATGGRPRYPTN                ISGATEHGITSDDIFWLKKSPGKT       
              -------------------------caacagaaagggaggccatcaa                atggagcgaaaggattcaatcgaa       
              -------------------------acttccaatttccgggcgacca                tcgccaagtcgaattgtaaccgac       
              -------------------------ggcgtcgctgccagggcgccat                ccactgcccctccccggagatga        
                                                                                                            

Query   tron---> LVVGASYVSLECAGFLTGVGLDTAVMMRSIPLRGFDQ <---Intron---> QMASLVTEHMESYGTKFLKKCVPMKVEKLESGRLQVTW
        22bp   >      | |/|||||||||/|||| ||/||| |||||| <    96bp    > ||| |||//||/|||||  |||| /|/|| || |||||
Target           TQC-CSDVALECAGFLTGLGLDTTVMVRSIALRGFDQ                QMAGLVTDYMEAYGTKFAWKCVPKRVDKLSSGALQVTW
                 act-ttgggcgtggtcagcgtgaagagcaagccgtgc                caggcgagtaggtgaatgtatgcaaggacttggccgat
                 cag-gcatctagcgttcgtgtacctttggtctggtaa                atcgttcaatacagcatcgagtcagtaatccgctatcg
                acgt-catgttgtacccactcgccaggtcctccggttg                agatacaccgggtgcgtaggtcggagcaggaatggggg
                                                                                                            

Query   KNTDLGTEEMDSFDTVMWAVG <---Intron---> RVPDSETLNLEIVGVKTNSETGKIIVDASEATSVPHIYAIGDITE <---Intron---> GR
         /   | |  ||/|/|/|||| <   5492bp   > | |/// | |/ /||/ | |/|||// | |/||||/||| ||| / <   1463bp   > ||
Target  TDKHTGKEHQDSYDSVLWAVG                RAPETKALGLDKLGVQLNKESGKIVLGADESTSVPNIYAFGDIGQ                GR
        agacagagccgttgtgttggg                agcgaagcgcgacggccaagtgaagtggggtatgcaatgtggagc                gc
        caaacgaaaaacaacttgct                ggccacactgtaatgtataaacgatttgcaaccctcatactgatga                gg
        tcgcgcaacgcccctgagat                caatacacgcgcgttgaccgggaaatattcaacggaccctctcccg                tt
                                                                                                            

Query   PELTPTAIAAGKLLARRLFGHSSELMDYDN <---Intron---> VPTTVFTPLEYGCVGLSEEKAVQCYGSDNVE <---Intron---> VFHAYYK
        |||||||| ||||||||| | |/|||/||| <   430bp    > |||||||||||||||||||/| / /| | || <   1251bp   > |/||/||
Target  PELTPTAIKAGKLLARRLTGLSTELMNYDN                VPTTVFTPLEYGCVGLSEEEAEKRHGKDGVE                VYHAFYK
        cgcacagaaggaccgcacagcaagcaatga                gcaagtaccgtgtggctgggggaacgagggg                gtcgtta
        catcccctacgattcggtcgtgcattaaaa                tcccttcctaaggtgtcaaacaagagaagta                taactaa
        tagcaaccagagtgccagttccagcgcctc                gccagccccgcctgtgtgggtgggtaacccg                tcctccg
                                                                                                            

Query   PLEFTAAERDAAQCYMK <---Intron---> MVCLREREQRILGLHFIGPNAGEVIQGFALGIK <---Intron---> CGATYPQLMKTIGIHPTC
        ||||| |||||/|||/| <   363bp    > //| |  ||/|||||| ||||||| |||||| | <   607bp    > |||||| |//|/||||||
Target  PLEFTVAERDASQCYLK                VICERGGEQKILGLHFTGPNAGEVTQGFALGFK                CGATYPHLLQTVGIHPTC
        ccgtagggcggacttta                gatgcgggcaacgcctagcaggggacgtgtgta                tggatcccccaggaccat
        ctatctcagacgagata                ttgagggaaattgtatcgcacgatcagtctgta                ggccacattactgtaccg
        tgactcagctccgtcag                gttgtaagggcgtgccttactaacagcttgcc                gtaaatccggggacccact
                                                                                                            

Query   AEEITKLHITKRSGLDATVTGCUG
        |||/||//||||||||||||||||
Target  AEEVTKVNITKRSGLDATVTGCUG
        ggggaagaaaactgcggagagttg
        caatcatatcagcgtacctcgggg
        cgggcgcccagcccgccgcaccat
                              * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 2049 ; UGA-SECIS: 2052

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = WARS01000015.1:subseq_17447025,200000_:subseq_0,120000_ Strand = + Positions = 112645 - 112716
 Found by:  Infernal (score=43.51) Covels (score=41.09)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -25.23

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((---....{[[{({((((((((.................))))))))})}]]}..--..-.)))))))..
 target  GUCGGCCAG---CUAAUGAUGACCUGCACUAAAACCCAAAACUGGGGAGUGCAGGCCUGAUGU--AA-CCUGGCCGCC
                         ****          ^^^                        ****