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

 Blastx evalue: 1e-14
 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/84952701/tempfiles/temptarget.fasta
 Chromosome: JACSYO010001694.1:subseq_1687072,100000_ Strand: +
 Positions:
 -Exon 1  50314        50459
 -Exon 2  51126        51201
 -Exon 3  53080        53136
 -Exon 4  53399        53470
 -Exon 5  57772        57870
 -Exon 6  57962        58136
 -Exon 7  64006        64142
 -Exon 8  65904        65999
 -Exon 9  66569        66661
 -Exon 10 68405        68476
 -Exon 11 69174        69271
 -Exon 12 69800        69926

 Redox box: no

Query   GTKWGLGGTCVNVGCIPKKLMHQAALLGGALKDAQHYGWSMAHPVHHSW <---Intron---> SVMAQAVQNYVKSLNWGHRVQLQDK <---Intro
        |||||||||||||||||||||||||||| |/|||/ ||| // |/ | | <   666bp    > / ||/|/||/|/||||||||||||| <   1878b
Target  GTKWGLGGTCVNVGCIPKKLMHQAALLGTAVKDAKKYGWQISGPICHDW                ATMAEAIQNHVRSLNWGHRVQLQDK          
        gaatgcggatgaggtacaacaccggccgaggaggaatgtcatgcatcgt                gaagggacacgattatgcagcccga          
        gcaggtggcgtatggtcaattaaccttgcctaacaaaggatcgctgaag                cctcactaaatgctaggagtataaa          
        tcggtttaattttcctcggcgcgttatctacattggtcggcagacttc                gccgagttacccgtgcgtcatgcgcg          
                                                                                                            

Query   n---> KVKYFNMKGSFLDSHTVCGLAKGGKKTTLTAEKIVIATGGRPKYPTH <---Intron---> ITGALEYGITSDDLFWLKDSPGKT <---In
        p   >                             |||/ ||||||||| |||  <   262bp    > | || |/|/||||/|||  ||||| <   43
Target        ----------------------------LTAKNIVIATGGRPNYPTK                IPGATEHGMTSDDIFWLNKSPGKT       
              ----------------------------cagaaagagaggccatcaa                acggagcgaaaggattcaatcgaa       
              ----------------------------tccaatttccgggcaacca                tcgccaagtcgaattgtaaccgac       
              ----------------------------gtcgctgccatagctccag                caaaggcagctccccggcggtgag       
                                                                                                            

Query   tron---> LVVGASYVSLECAGFLTGVGLDTAVMMRSIPLRGFDQ <---Intron---> QMASLVTEHMESYGTKFLKKCVPMKVEKLESGRLQVTW
        01bp   >      | |/|||||||||||||| ||/||| |||||| <    91bp    > |/| |||//| /|||||  ||||  |/|| || |||||
Target           ----CSDVALECAGFLTGVGLDTTVMVRSIALRGFDQ                QIAGLVTDYMAAYGTKFAWKCVPKSVDKLSSGALQVTW
                 ----ttgggcgtggtcagggtgaagagcaagccgtgc                caggcgagtaggtgaatgtatgcaaggacttggccgat
                 ----gcatctagcgttcgtgtacctttggtctggtaa                atcgttcaatccagcatcgagtcagtaatccgctatcg
                 ----catgtggtaccccctcgccaggccctccggttg                atatacaccgcatgcgtaggtcagtgcatcaacgggcg
                                                                                                            

Query   KNTDLGTEEMDSFDTVMWAVG <---Intron---> RVPDSETLNLEIVGVKTNSETGKIIVDASEATSVPHIYAIGDITE <---Intron---> GR
         /|  | /  |//|/|/|||| <   5869bp   > | |/// | |/ /|//   ||||||/ | |/||||/||| ||| | <   1761bp   > ||
Target  TDTHTGNDHKDTYDSVLWAVG                RAPETKALGLDKLGMQLKKETGKIILGADESTSVPNIYAFGDIGE                GR
        agacagagcagatgtgttggg                agcgaagcgcgacgaccaagagaaatggggtatgcaatgtggagg                gc
        cacacgaaaaacaacttgct                ggccacactgtaatgtataaacgatttgcaaccctcatactgatga                gg
        ccccaccccgctcccgagat                cactacacgcgcgtcgacaggggaatgcgcaccggatcttttcccg                tt
                                                                                                            

Query   PELTPTAIAAGKLLARRLFGHSSELMDYDN <---Intron---> VPTTVFTPLEYGCVGLSEEKAVQCYGSDNVE <---Intron---> VFHAYYK
        |||||||| ||/|||||| |||/|||/||| <   569bp    > |||||||||||||||||||/| / /| | /| <   1743bp   > |/||/||
Target  PELTPTAIKAGRLLARRLAGHSTELMNYDN                VPTTVFTPLEYGCVGLSEEEAEKRHGKDGIE                VYHAFYK
        cgtacagaaggaccgcatggcaagcaatga                gcaagtaccgtgtggctgggggaacgaggag                gtcgtta
        catcccctacggttcggtcgagcattaaaa                tcccttcctaaggtgtcaaacaagagaagta                taactaa
        tagcagctagagtcctagtaccgacgccct                gcctgccctgcctgtgtgggtgggtggcctg                ccctcca
                                                                                                            

Query   PLEFTAAERDAAQCYMK <---Intron---> MVCLREREQRILGLHFIGPNAGEVIQGFALGIK <---Intron---> CGATYPQLMKTIGIHPTC
        ||||| |||||/|||/| <   697bp    > /|| |  ||/|||||| ||||||| ||||/| / <   528bp    > |||||  |//|/||||||
Target  PLEFTVAERDASQCYLK                VVCERGGEQKILGLHFTGPNAGEVTQGFAMGFQ                CGATYSHLLQTVGIHPTC
        ccgtagggcggacttta                ggtgcgggcaacgtctagcaggggacgtgagtc                tggattcctcaggaccat
        ctatctcagacgagata                ttgagggaaattgtatcgcacgatcagtctgta                ggccacattactgtaccg
        tgacttagctccgtcag                gatggtagggcgtgctctacgaacagcttgcc                gtaaattcggaagcccact
                                                                                                            

Query   AEEITKLHITKRSGLDATVTGCUG
        |||/ |///|||||||||||||||
Target  AEEVIKVNVTKRSGLDATVTGCUG
        ggggaagagaactgtggagagttg
        caattatatcagcgtacctcgggg
        cgggcgcccaggccgccgacccat
                              * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 2151 ; UGA-SECIS: 2154

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = JACSYO010001694.1:subseq_1687072,100000_ Strand = + Positions = 72078 - 72149
 Found by:  Infernal (score=47.22) Covels (score=41.84)
 Stem2 length = 10   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -29.83

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..(((((((---....{[[{((((((((((.................))))))))))}]]}..--..-.)))))))..
 target  GUCGGCCAG---AUAAUGAUGGCCUGCACUAAAACCCAAAACUGGGAAGUGUAGGCCUGAUGU--CA-CCUGGCCGCC
                         ****          ^^^                        ****