_________________________________.______________________._________________________________________________________________________________
_|*|_|*|_|*|_|*|_|*|_|*|_|*|_|*| |       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/520446604/tempfiles/temptarget.fasta
 Chromosome: KV884700.1:subseq_1009562,100000_ Strand: +
 Positions:
 -Exon 1  50006        50151
 -Exon 2  53760        53835
 -Exon 3  55798        55854
 -Exon 4  56096        56173
 -Exon 5  61214        61303
 -Exon 6  61380        61554
 -Exon 7  67536        67672
 -Exon 8  68932        69022
 -Exon 9  69565        69662
 -Exon 10 71050        71121
 -Exon 11 71278        71375
 -Exon 12 71780        71906

 Redox box: no

Query   GTKWGLGGTCVNVGCIPKKLMHQAALLGGALKDAQHYGWSMAHPVHHSW <---Intron---> SVMAQAVQNYVKSLNWGHRVQLQDK <---Intro
        ||/||||||||||||||||||||||||| |/|||  ||| // ||/| | <   3608bp   > / ||/||||/||||||||||||||| <   1962b
Target  GTRWGLGGTCVNVGCIPKKLMHQAALLGTAVKDATKYGWQISGPVYHDW                ATMAEAVQNHVKSLNWGHRVQLQDK          
        gaatgcggatgaggtacaacaccggccgaggaggaatgtcatgcgtcgt                gaaggggcacgatcatgcagcccga          
        gcgggtggcgtatggtcaattaaccttgcctaaccaaggatcgctaaag                cctcactaaatactaggagtataaa          
        tcagttttatttgctttggcgtgatatcttcattagccggcaggcctc                gccgggctactcgcgcgtcatgcgcg          
                                                                                                            

Query   n---> KVKYFNMKGSFLDSHTVCGLAKGGKKTTLTAEKIVIATGGRPKYPTH <---Intron---> ITGALEYGITSDDLFWLKDSPGKTLV <---
        p   >                             |||/ |||||||||||||/ <   241bp    > | ||/|/|/||||/|||| ||||| | <   
Target        ----------------------------LTAKNIVIATGGRPKYPTN                IPGAMEHGLTSDDIFWLKKSPGKTCV     
              ----------------------------cagaaagagaggccatcaa                acggagcgcaaggattcaatcgaatg     
              ----------------------------tccaatttccgggcaacca                tcgctaagtcgaattgtaaccgacgt     
              ----------------------------gtcgctgtcatagcgccat                ctacggccccctcatggagataagta     
                                                                                                            

Query   Intron---> VGASYVSLECAGFLTGVGLDTAVMMRSIPLRGFDQ <---Intron---> QMASLVTEHMESYGTKFLKKCVPMKVEKLESGRLQVTW
        5040bp   >      |/|||||||||||||| ||/||| |||||| <    76bp    > ||| |||//||/|||||  /||| /|/|| || |||||
Target             -----VALECAGFLTGVGLDTTVMVRSIALRGFDQ                QMAGLVTDYMEAYGTKFAWQCVPKRVDKLSSGALQVTW
                   -----ggcgtggtcagggtgaagagcaagccgtgc                caggtgagtaggtgaatgtctgcaaggacttggccgat
                   -----tctagcgttcgtgtacctttggtctggtaa                atcgttcaatacagcatcgagtcagtaatccgctatcg
                   -----gtggtatccacccgccaggtcccccggttg                agatgggccggttgcgtagatctgagcacaaactggcg
                                                                                                            

Query   KNTDLGTEEMDSFDTVMWAVG <---Intron---> RVPDSETLNLEIVGVKTNSETGKIIVDASEATSVPHIYAIGDITE <---Intron---> GR
         ||  |/|  ||/|/|/|||| <   5981bp   > | |/// | |/ /||/ | |||||/| | |/||||/||| ||| | <   1259bp   > ||
Target  TNTQTGSEHDDSYDSVLWAVG                RAPETKALGLDKLGVQLNKETGKIVVGADESTSVPNIYAFGDIGE                GR
        aaacagagcggatgtgctggg                agcgaagcgcgacggccaagagaaggggggtatgcaatgtggagg                gc
        cacacggaaaagaacttgct                ggccacactgtaatgtataaacgatttgcaaccctcatactgatga                gg
        cccgaacgcccccctgggat                tactacacgcccgctgaccggggaatgctcacccgaccttttctcg                tt
                                                                                                            

Query   PELTPTAIAAGKLLARRLFGHSSELMDYD <---Intron---> NVPTTVFTPLEYGCVGLSEEKAVQCYGSDNVE <---Intron---> VFHAYYK
        |||||||| ||||||||| |  /||//   <   542bp    >  |||||||||||||||||||/| / /| | /| <   1387bp   > |/||/||
Target  PELTPTAIKAGKLLARRLAGARTELLNQC                QVPTTVFTPLEYGCVGLSEEEAERRHGEDGIE                VYHAFYK
        cgtacagaaggaccgcacgggaagccact                cgcaagtaccgtgtggctgggggaacggggag                gtcgtta
        catcccctacgattcggtcgcgcattaa                gatcccttcctaaggtgtcaaacaggagaagta                taactaa
        tagcaactaaagtgccagtggaagcgca                tggccagccttgtctacatgggaggataaccag                tcctccg
                                                                                                            

Query   PLEFTAAERDAAQCYMK <---Intron---> MVCLREREQRILGLHFIGPNAGEVIQGFALGIK <---Intron---> CGATYPQLMKTIGIHPTC
        ||||| || || |||/| <   156bp    > /|| |   |/|||||| ||||||| ||||/|   <   404bp    > |||||  |//|/||||||
Target  PLEFTVAECDAGQCYIK                VVCERGGNQKILGLHFTGPNAGEVTQGFAMGFH                CGATYSHLLQTVGIHPTC
        ccgtagggtgggcttaa                ggtgcggacaacgcctagcaggggacgtgagtc                tggattcctcaggaccat
        ctatctcagacgagata                ttgagggaaattgtatcgcacgatcagtctgta                ggccacattactgtaccg
        tgactttgttacgtcag                gatgatacggcatgccacataaacagcttgcc                ctagatccgggaacccact
                                                                                                            

Query   AEEITKLHITKRSGLDATVTGCUG
        |||/ |//||||||||||||||||
Target  AEEVVKVNITKRSGLDATVTGCUG
        gggggagaaaactgtggagagttg
        caattatatcagcgtacctcgggg
        tgggcggctggcctgccaccccat
                              * 
 Sequence until next stop: 
TAA
 * 

 Distance CDS-SECIS: 1955 ; UGA-SECIS: 1958

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = KV884700.1:subseq_1009562,100000_ Strand = + Positions = 73862 - 73933
 Found by:  Infernal (score=34.26) Covels (score=39.0)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -12.03

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ..((({({(---....{[[{({((((((((.................))))))))})}]]}..--..-.)})})))..
 target  GUCGGCCAG---CUAAUGAUGACCUGCAUUAAAACCCAAAGCUGGGGAGUGCAGGCCUGAUGU--CA-CCCGCCCGCC
                         ****          ^^^                        ****