Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001417.1 Corchorus capsularis cultivar CVL-1 contig01417, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 828

Length: 1380
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28


Found at i:101 original size:46 final size:43

Alignment explanation


    Indices: 32--329  Score: 327
    Period size: 40  Copynumber: 6.9  Consensus size: 43

         22 ACTAGGAAGC

                            *                        * 
         32 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAATAAGT
          1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAACT

                                 *        *                   
         75 AGGTAAACAACACCTTCCGATAAGGAAGGGTAAACTGGGAATAGGCAAC-
          1 ---TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT----AACT

                                                        
        124 TAAACAACACCTTCCGAT-AGGGAAGGGCAAACTGGG---AACT
          1 TAAACAACACCTTCCGATGA-GGAAGGGCAAACTGGGAATAACT

                                       *                   
        164 TAAACAACACCTTCCGATGAGGAAGGGAAAACTGGGAATAGGCAAC-
          1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT----AACT

                                                        
        210 TAAACAACACCTTCCGAT-AGGGAAGGGCAAACTGGG---AACT
          1 TAAACAACACCTTCCGATGA-GGAAGGGCAAACTGGGAATAACT

                                                       
        250 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGG---AACT
          1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAACT

                                                     
        290 TAAACAACACCTTCCGATGAGGAAGGGCAAAAC-GGGAATA
          1 TAAACAACACCTTCCGATGAGGAAGGGC-AAACTGGGAATA

        330 GGAAACAACT


Statistics
Matches: 224,  Mismatches: 7, Indels: 45
        0.81            0.03        0.16

Matches are distributed among these distances:
  39    6  0.03
  40  102  0.46
  41    6  0.03
  43    1  0.00
  45    2  0.01
  46  102  0.46
  47    3  0.01
  50    2  0.01

ACGTcount: A:0.39, C:0.20, G:0.26, T:0.14


Consensus pattern (43 bp):   
TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATAACT

Found at i:189 original size:86 final size:86

Alignment explanation


    Indices: 31--287  Score: 399
    Period size: 86  Copynumber: 2.9  Consensus size: 86

         21 AACTAGGAAG

                             *                         *                     
         31 CTAAACAACACCTTCCGGT-GAGGAAGGGCAAACTGGGAATAAGTAGGTAAACAACACCTTCCGA
          1 CTAAACAACACCTTCCGATAG-GGAAGGGCAAACTGGG---AACT---TAAACAACACCTTCCGA

             *        *                 
         95 TAAGGAAGGGTAAACTGGGAATAGGCAA
         59 TGAGGAAGGGAAAACTGGGAATAGGCAA

                                                                             
        123 CTAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGATGAGGAA
          1 CTAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGATGAGGAA

                                 
        188 GGGAAAACTGGGAATAGGCAA
         66 GGGAAAACTGGGAATAGGCAA

                                                                             
        209 CTAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGATGAGGAA
          1 CTAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGATGAGGAA

               *          
        274 GGGCAAACTGGGAA
         66 GGGAAAACTGGGAA

        288 CTTAAACAAC


Statistics
Matches: 159,  Mismatches: 5, Indels: 8
        0.92            0.03        0.05

Matches are distributed among these distances:
  86  121  0.76
  89    3  0.02
  92   34  0.21
  93    1  0.01

ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14


Consensus pattern (86 bp):   
CTAAACAACACCTTCCGATAGGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGATGAGGAA
GGGAAAACTGGGAATAGGCAA

Found at i:456 original size:47 final size:46

Alignment explanation


    Indices: 293--462  Score: 146
    Period size: 46  Copynumber: 3.6  Consensus size: 46

        283 GGGAACTTAA

                                         ***          *      *
        293 ACAACACCTTCCGA-TGAGGAAGGGCAAAACGGGAATAGGAAACAACTAA
          1 ACAACACCTTCCGACTG-GGAAGGGCAAATTAGGAAT---AAGCAACTAG

               *           *           *  *               
        342 ACAGCACCTTCCGACGGGGAAGGGCAACTTGGGAATAAGCAACTAG
          1 ACAACACCTTCCGACTGGGAAGGGCAAATTAGGAATAAGCAACTAG

                          *                       **      * 
        388 ACAACACCTTCC-AGTGGGGAAGGGCAAATTAGGAATTTGGCAACTGG
          1 ACAACACCTTCCGACT-GGGAAGGGCAAATTAGGAA-TAAGCAACTAG

                            *           
        435 ACAACACCTTCCGACTAGGAAGGGCAAA
          1 ACAACACCTTCCGACTGGGAAGGGCAAA

        463 ACCGGAAATT


Statistics
Matches: 100,  Mismatches: 17, Indels: 10
        0.79            0.13        0.08

Matches are distributed among these distances:
  45    1  0.01
  46   36  0.36
  47   31  0.31
  48    2  0.02
  49   29  0.29
  50    1  0.01

ACGTcount: A:0.37, C:0.22, G:0.27, T:0.14


Consensus pattern (46 bp):   
ACAACACCTTCCGACTGGGAAGGGCAAATTAGGAATAAGCAACTAG

Found at i:1148 original size:32 final size:32

Alignment explanation


    Indices: 1102--1165  Score: 94
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       1092 ATTTCATCAT

                     *             *         
       1102 TTACTTAAAGGTTCAAT-TTTTATTTACAAAAA
          1 TTACTTAAAAGTTCAATGTTTTAATTA-AAAAA

                                            
       1134 TTACTTAAAAGTTCAATGTTTTAATTAAAAAA
          1 TTACTTAAAAGTTCAATGTTTTAATTAAAAAA

       1166 CTCAATCATT


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  32   21  0.72
  33    8  0.28

ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42


Consensus pattern (32 bp):   
TTACTTAAAAGTTCAATGTTTTAATTAAAAAA
Done.