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

 Blastx evalue: 8e-16
 Query name: gi|148277083|ref|NP_001080052.1| thioredoxin reductase 2 [Xenopus laevis]
 Query range: 18-504  (total 504)

 Target: /data/www-rg/seblastian_results/726135928/tempfiles/temptarget.fasta
 Chromosome: SSNR01000064.1:subseq_1978300,119972_ Strand: +
 Positions:
 -Exon 1  49997        50057
 -Exon 2  50143        50199
 -Exon 3  50299        50443
 -Exon 4  50831        50905
 -Exon 5  53651        53729
 -Exon 6  55243        55305
 -Exon 7  55378        55448
 -Exon 8  60020        60131
 -Exon 9  60205        60379
 -Exon 10 64731        64867
 -Exon 11 66892        66987
 -Exon 12 67480        67572
 -Exon 13 68647        68718
 -Exon 14 68973        69070
 -Exon 15 69846        69972

 Redox box: no

Query   HDYDLLVIGGGSGGLACAKQA <---Intron---> AQFGKKVAVFDYVEPSPRG <---Intron---> TKWGIGGTCVNVGCIPKKLMHQAALIGS
        /||||/|||||||||||/|/| <    85bp    > || |/|||| |||||||/| <    99bp    > ||||/||||||||||||||||||||/|/
Target  YDYDLVVIGGGSGGLACSKEA                AQLGQKVAVLDYVEPSPKG                TKWGLGGTCVNVGCIPKKLMHQAALLGT
        tgtgtggagggtggcgttagg                gccgcagggcgtggctcag                aatgcggatgaggtacaacaccggccga
        aaaattttgggcggtcgcaa                ccatgaatcttaataccca                gcaggtggcgtatggtcaattaaccttgc
        cctcggttttatacgcccaa                gaggagatttattggatta                tcggtcttgtctgccttggcgtattcttt
                                                                                                            

Query   TMKDAPHYGWGTPYEIQHDW <---Intron---> GKMAGAVQNYVKSLNWGHRIQLQDK <---Intron---> KVKYFNLKANFVDEHCIRGVTKA
         /|||  |||  |  / ||| <   387bp    >   || /|||/|||||||||/||||| <   2745bp   > |||| ||| / |||| /||//||
Target  AVKDAKKYGWQIPERVCHDW                TTMAESVQNHVKSLNWGHRVQLQDK                KVKYLNLKGSLVDEHTVRGLSKA
        ggaggaatgtcacgagtcgt                aaaggtgcacgattatgcagcccga                agatcacagacgggcagagcaag
        ctaacaaaggatcagtgaag                cctcactaaatactaggagtataaa                ataatataggttaaactggtgac
        tcattggtcggaagatctc                gccgaattgcccgtacgtcgcgcac                gagatgtaactggtacacaagcac
                                                                                                            

Query   GKE <---Intron---> TLVTAQNIVIATGGRPKYPTH <---Intron---> VPGALEYGITSDDLFWLKESPGKT <---Intron---> LVVG
        ||| <   1513bp   > |//|//|/| ||||||||| | <    72bp    > /|||/|/||||||||||//||||| <   4571bp   >     
Target  GKE                TILTSKNVVFATGGRPKYPIH                IPGAMEHGITSDDLFWLEKSPGKT                SACF
        gag                aacataaggtgaggccatcac                acggagcgaaaggtttcgatcgaa                tgtt
        gaa                cttccaatttccgggcaacta                tcgctaagtcgaattgtaaccgac                ccgt
        aag                acgccgttgccatagcaccat                ctagggcccctttacgtggcaaa                cacct
                                                                                                            

Query   ASYVSLECAGFLTGIGLNTTAMVRSIPLRGFDQ <---Intron---> QMAYLVADYMESHGTKFLWKCTPSHVEKLKNGKLQVTWKNTQSGKEGVDIY
         / |/||||||||||||/|| ||||| |||||| <    73bp    > ||| || ||||//||/||||  |  |/|| /| ||||| ||//| |  | |
Target  YTDVALECAGFLTGIGLDTTVMVRSIALRGFDQ                QMAGLVTDYMEAYGTRFLWKSVPKRVDKLSSGGLQVTWTNTETGSEHEDTY
        tagggcgtggtcagagtgaagagcaagccgtgc                caggcgagtaggtgaatttatgcaaggacttggccgataaagagagcggat
        acatctagcgttcgtgtacctttggtctggtaa                atcgttcaatacagcgttgactcagtaatccggtatcgcacacggaaaaca
        catgttgtattcacccgccaggtcccccgtttg                agaccgatcgatcacgtgggccaaagcggttacgggggcctggccgcaccc
                                                                                                            

Query   DTVMWAVG <---Intron---> RAAETQYLNLEKVGVKIKPETGKIIVDASEATSVPHIYAIGDITE <---Intron---> GRPELTPTAIAAGKL
        |/|/|||| <   4351bp   > || ||/ | |/|/||//  |||||/| | |/||||//|| |||/| <   2024bp   > |||||||||| ||||
Target  DSVLWAVG                RAPETKALGLDKLGVQLNKETGKIVVGADESTSVPNVYAFGDISE                GRPELTPTAIKAGKL
        gtgttggg                cgcgaagcgcgacggccaagagaaggggggtatgcagtgtggaag                gccgtacagaaggac
        acttgct                ggccacactgtaatgtataaacgatttgcaaccctcatactgatga                ggcatcccctacgat
        cggaggt                tattacacacccgtcggccggggaatgcttacctgacctcctcctg                tttggcagctagagc
                                                                                                            

Query   LAIRLFSGSAELMDYDS <---Intron---> VPTTVFTPLEYGCVGISEEEAKERYGDDNIE <---Intron---> VFHAFYKPLEFTVAERDASQ
        || ||   |//||/||/ <   492bp    > | |||||||||||||/||||| /|/|/| /| <   1074bp   > |/||||||||||||||||||
Target  LAQRLAGQSSDLMNYDN                VATTVFTPLEYGCVGLSEEEAVKRHGEDGVE                VYHAFYKPLEFTVAERDASQ
        cgcacggcatgcaatga                ggaagtaccgtgtggctgggggaacgggggg                gtcgttaccgtagggcggac
        tcagtcgagcattaaaa                tcccttcctaaggtgtcaaactagagaagta                taactaactatctcagacga
        ccaggttgcttcgctcc                gcgagcctggcctgtgagggtgggcaataag                ttttccgtaacttagctccg
                                                                                                            

Query   CYIK <---Intron---> IICLRKHDQRILGLHLTGPNAGEVIQGFALGIK <---Intron---> CGATYPQLMCTVGIHPTCAEEVTKLHITKRS
        |||| <   254bp    > /|| |  ||/|||||  |||||||||||//|// <   775bp    > ||||| ||/ |||||||||||/ |/||||||
Target  CYIK                VICERGGDQKILGLHFIGPNAGEVIQGFSVGLQ                CGATYSQLLQTVGIHPTCAEEMVKIHITKRS
        ttaa                gatgcgggcaacgcctagcaggggacgttggtc                tggattccccaggaccatgggagaacaaact
        gata                ttgagggaaattgtattgcacgattagtctgta                ggccacattactgtaccgcaattatatcagc
        ccag                gttgttttggtatgctctactagcagcttgca                atagtttggcgtaaccggtcgggcgcccggct
                                                                                                            

Query   GLDPTVTGCUG
        |||||||||||
Target  GLDPTVTGCUG
        gtgcagagttg
        gtacctcgggg
        aacggctccat
                 * 
 Sequence until next stop: 
TAG
 * 

 Distance CDS-SECIS: 1793 ; UGA-SECIS: 1796

------- SECIS element -- id:1 -- grade:A ----
 Chromosome = SSNR01000064.1:subseq_1978300,119972_ Strand = + Positions = 71766 - 71839
 Found by:  Infernal (score=38.92) Covels (score=39.63)
 Stem2 length = 9   Apical loop length = 17   Insertion in stem2 = 0, 0
 Free Energy = -23.93

         ..(((((((.......(((((((((((((((...............)))))))))))))))........)))))))..
 model   uucggucaugcgUuaAUGAcGgccuggcccuAAAcCcuuuuuggggcgggccaggcCuGAUGuuuuuucaugaccggc
         ....((((((--....{[[{({((((((((.................))))))))})}]]}..--...))))))....
 target  CGACGGCCAG--CUAAUGAUGACCUGCGCUAAAACCCAAAACUGGGGAGUGCAGGCCUGAUGU--CACCUGGCCACAA
                         ****          ^^^                        ****