Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006131.1 Corchorus capsularis cultivar CVL-1 contig06149, 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: 17338
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33


Found at i:20 original size:2 final size:2

Alignment explanation


    Indices: 15--42  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

          5 TGTGTGTGTG

                                                     
         15 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         43 GGTGATTAGC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:716 original size:2 final size:2

Alignment explanation


    Indices: 709--734  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

        699 GCCTTTCAAA

                                                  
        709 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

        735 CTCCTTCAAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:7093 original size:21 final size:21

Alignment explanation


    Indices: 7067--7106  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       7057 ACCCGTCGAC

                                 
       7067 GAAGACAAAGGGAGAAGCGAT
          1 GAAGACAAAGGGAGAAGCGAT

                  *            
       7088 GAAGACGAAGGGAGAAGCG
          1 GAAGACAAAGGGAGAAGCG

       7107 GAGCATATGA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.45, C:0.10, G:0.42, T:0.03


Consensus pattern (21 bp):   
GAAGACAAAGGGAGAAGCGAT

Found at i:8754 original size:60 final size:60

Alignment explanation


    Indices: 8658--8791  Score: 180
    Period size: 60  Copynumber: 2.2  Consensus size: 60

       8648 GTTAACCTAC

                     *                 *   *                  *     *   
       8658 ACGAAAATGTTCAATTTAGGGTCCATGTTTTTAATTTGGTTAAATAGGGTTCTAACGTAA
          1 ACGAAAATGCTCAATTTAGGGTCCATGCTTTGAATTTGGTTAAATAGGGTCCTAACATAA

                                                                        *
       8718 ACGAAAATGCTCAATTTAGGG-CACATGCTTTGAATTTGGTTAAATAGGGTCCTAACATAT
          1 ACGAAAATGCTCAATTTAGGGTC-CATGCTTTGAATTTGGTTAAATAGGGTCCTAACATAA

            *       *     
       8778 GCGAAAATACTCAA
          1 ACGAAAATGCTCAA

       8792 ATAAGGGACT


Statistics
Matches: 65,  Mismatches: 8, Indels: 2
        0.87            0.11        0.03

Matches are distributed among these distances:
  59    1  0.02
  60   64  0.98

ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33


Consensus pattern (60 bp):   
ACGAAAATGCTCAATTTAGGGTCCATGCTTTGAATTTGGTTAAATAGGGTCCTAACATAA

Found at i:8947 original size:61 final size:60

Alignment explanation


    Indices: 8850--8982  Score: 194
    Period size: 61  Copynumber: 2.2  Consensus size: 60

       8840 TTTGCATATA

                    *   *               *                               
       8850 TTAGGGCCTTATTTAACCAAATTAAAAGTACAAGTCCTAAATTGAGCATTTTCACATACG
          1 TTAGGGCCCTATCTAACCAAATTAAAAGCACAAGTCCTAAATTGAGCATTTTCACATACG

                                    *      *                       *     
       8910 TTAGGGCCCTATACTAACCAAATTCAAAGCATAAGTCCTAAATTGAGCATTTTCATATACG
          1 TTAGGGCCCTAT-CTAACCAAATTAAAAGCACAAGTCCTAAATTGAGCATTTTCACATACG

                  *     
       8971 TTAGGGACCTAT
          1 TTAGGGCCCTAT

       8983 TTGAGCAATT


Statistics
Matches: 65,  Mismatches: 7, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  60   11  0.17
  61   54  0.83

ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31


Consensus pattern (60 bp):   
TTAGGGCCCTATCTAACCAAATTAAAAGCACAAGTCCTAAATTGAGCATTTTCACATACG

Found at i:17283 original size:2 final size:2

Alignment explanation


    Indices: 17278--17331  Score: 108
    Period size: 2  Copynumber: 27.0  Consensus size: 2

      17268 GTAAAAAAGG

                                                                          
      17278 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

                             
      17320 GA GA GA GA GA GA
          1 GA GA GA GA GA GA

      17332 TGATGAG


Statistics
Matches: 52,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   52  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
GA

Done.