Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007957.1 Corchorus capsularis cultivar CVL-1 contig07978, 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: 19709
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30


Found at i:6947 original size:45 final size:45

Alignment explanation


    Indices: 6883--6968  Score: 154
    Period size: 45  Copynumber: 1.9  Consensus size: 45

       6873 TTCTTCAAAT

                  * *                                    
       6883 AAGAACGTGGGTGGTTACCTCATTCTTGATGAAGTAACTGCTTTG
          1 AAGAACCTAGGTGGTTACCTCATTCTTGATGAAGTAACTGCTTTG

                                                     
       6928 AAGAACCTAGGTGGTTACCTCATTCTTGATGAAGTAACTGC
          1 AAGAACCTAGGTGGTTACCTCATTCTTGATGAAGTAACTGC

       6969 CTATTGGCTT


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  45   39  1.00

ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31


Consensus pattern (45 bp):   
AAGAACCTAGGTGGTTACCTCATTCTTGATGAAGTAACTGCTTTG

Found at i:7035 original size:31 final size:31

Alignment explanation


    Indices: 6992--7124  Score: 212
    Period size: 31  Copynumber: 4.3  Consensus size: 31

       6982 AATACTTGGT

                *             *            
       6992 GAGTGTTTACGGTATACCTTTGGTGGGTAGG
          1 GAGTATTTACGGTATACCCTTGGTGGGTAGG

                                         * 
       7023 GAGTATTTACGGTATACCCTTGGTGGGTATG
          1 GAGTATTTACGGTATACCCTTGGTGGGTAGG

                                         * 
       7054 GAGTATTTACGGTATACCCTTGGTGGGTATG
          1 GAGTATTTACGGTATACCCTTGGTGGGTAGG

            *                 *            
       7085 AAGTATTTACGGTATACCTTTGGTGGGTAGG
          1 GAGTATTTACGGTATACCCTTGGTGGGTAGG

                     
       7116 GAGTATTTA
          1 GAGTATTTA

       7125 GTATTTGGGT


Statistics
Matches: 95,  Mismatches: 7, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   95  1.00

ACGTcount: A:0.20, C:0.11, G:0.33, T:0.36


Consensus pattern (31 bp):   
GAGTATTTACGGTATACCCTTGGTGGGTAGG

Found at i:12599 original size:19 final size:18

Alignment explanation


    Indices: 12566--12603  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

      12556 TTGAAATAAT

                   *          
      12566 TCTTCAATAATCTTCAAA
          1 TCTTCAAAAATCTTCAAA

                               
      12584 TCTTCAAAATATCTTCAAA
          1 TCTTCAAAA-ATCTTCAAA

             
      12603 T
          1 T

      12604 ACGAAATTCG


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    8  0.44
  19   10  0.56

ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39


Consensus pattern (18 bp):   
TCTTCAAAAATCTTCAAA

Found at i:13782 original size:19 final size:17

Alignment explanation


    Indices: 13749--13784  Score: 54
    Period size: 19  Copynumber: 2.0  Consensus size: 17

      13739 TTAAAAATTC

                             
      13749 TAAGCAATCATCAATCA
          1 TAAGCAATCATCAATCA

                               
      13766 TAAGCAAATCAATCAATCA
          1 TAAGC-AATC-ATCAATCA

      13785 ATATATATAC


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    5  0.29
  18    4  0.24
  19    8  0.47

ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22


Consensus pattern (17 bp):   
TAAGCAATCATCAATCA
Done.