Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012440.1 Corchorus capsularis cultivar CVL-1 contig12461, 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, 1000

Length: 63284
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:19263 original size:14 final size:14

Alignment explanation


    Indices: 19244--19272  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      19234 TGCTATCTTT

                          
      19244 GCAGTATGTTTTTA
          1 GCAGTATGTTTTTA

                          
      19258 GCAGTATGTTTTTA
          1 GCAGTATGTTTTTA

             
      19272 G
          1 G

      19273 TAATAATATC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.21, C:0.07, G:0.24, T:0.48


Consensus pattern (14 bp):   
GCAGTATGTTTTTA

Found at i:39126 original size:15 final size:15

Alignment explanation


    Indices: 39106--39134  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      39096 CTTTCAGCCT

                           
      39106 TTTGTTTTCATTTTC
          1 TTTGTTTTCATTTTC

                          
      39121 TTTGTTTTCATTTT
          1 TTTGTTTTCATTTT

      39135 TTAGGATTTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.07, C:0.10, G:0.07, T:0.76


Consensus pattern (15 bp):   
TTTGTTTTCATTTTC

Found at i:63031 original size:21 final size:21

Alignment explanation


    Indices: 63007--63063  Score: 105
    Period size: 21  Copynumber: 2.7  Consensus size: 21

      62997 GGAAAGGGGG

                                 
      63007 TTGCTAAATACCGCCCTAGTT
          1 TTGCTAAATACCGCCCTAGTT

                         *       
      63028 TTGCTAAATACCGTCCTAGTT
          1 TTGCTAAATACCGCCCTAGTT

                           
      63049 TTGCTAAATACCGCC
          1 TTGCTAAATACCGCC

      63064 GTGGCTGAAT


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  21   34  1.00

ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33


Consensus pattern (21 bp):   
TTGCTAAATACCGCCCTAGTT

Found at i:63250 original size:33 final size:33

Alignment explanation


    Indices: 63130--63234  Score: 183
    Period size: 33  Copynumber: 3.2  Consensus size: 33

      63120 GTAAAGGGCA

                  *                          
      63130 AGTGGGGAGGCTCAACCACGGCGGAGCCTCCCC
          1 AGTGGGAAGGCTCAACCACGGCGGAGCCTCCCC

                                             
      63163 AGTGGGAAGGCTCAACCACGGCGGAGCCTCCCC
          1 AGTGGGAAGGCTCAACCACGGCGGAGCCTCCCC

                                     *       
      63196 AGTGGGAAGGCTCAACCACGGCGGAACCTCCCC
          1 AGTGGGAAGGCTCAACCACGGCGGAGCCTCCCC

             *    
      63229 ACTGGG
          1 AGTGGG

      63235 GCGGCTTCGC


Statistics
Matches: 69,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  33   69  1.00

ACGTcount: A:0.21, C:0.35, G:0.34, T:0.10


Consensus pattern (33 bp):   
AGTGGGAAGGCTCAACCACGGCGGAGCCTCCCC
Done.