Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014861.1 Corchorus olitorius cultivar O-4 contig14894, 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: 18061
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:13617 original size:30 final size:31

Alignment explanation


    Indices: 13583--13646  Score: 76
    Period size: 30  Copynumber: 2.1  Consensus size: 31

      13573 CCGCAAATGA

                     *    *                
      13583 CAATTCAGGTTCTGTCGTTA-CCACGTGTGT
          1 CAATTCAGGATCTGACGTTATCCACGTGTGT

                 *                * *      
      13613 CAATTTAGGATCTGACGTTATCGAGGTGTGT
          1 CAATTCAGGATCTGACGTTATCCACGTGTGT

               
      13644 CAA
          1 CAA

      13647 AATAGGTGAA


Statistics
Matches: 28,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  30   17  0.61
  31   11  0.39

ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34


Consensus pattern (31 bp):   
CAATTCAGGATCTGACGTTATCCACGTGTGT

Found at i:14527 original size:24 final size:25

Alignment explanation


    Indices: 14500--14560  Score: 72
    Period size: 24  Copynumber: 2.5  Consensus size: 25

      14490 GTTTTAGGCT

                 *        *          
      14500 TGCTCCGTTTCTGGGGTTTGA-GAA
          1 TGCTCTGTTTCTGGAGTTTGAGGAA

                               *   * 
      14524 TGCTCTGTTTC-GGAGTTTTAGGCA
          1 TGCTCTGTTTCTGGAGTTTGAGGAA

                         
      14548 TGCTCTGTTTCTG
          1 TGCTCTGTTTCTG

      14561 TTAATTGTAT


Statistics
Matches: 31,  Mismatches: 4, Indels: 3
        0.82            0.11        0.08

Matches are distributed among these distances:
  23    7  0.23
  24   23  0.74
  25    1  0.03

ACGTcount: A:0.10, C:0.18, G:0.30, T:0.43


Consensus pattern (25 bp):   
TGCTCTGTTTCTGGAGTTTGAGGAA

Found at i:14681 original size:18 final size:18

Alignment explanation


    Indices: 14658--14709  Score: 86
    Period size: 18  Copynumber: 2.9  Consensus size: 18

      14648 ACCTTTCCAA

                              
      14658 TTTCCATACATAAACACC
          1 TTTCCATACATAAACACC

                      *   *   
      14676 TTTCCATACAAAAAGACC
          1 TTTCCATACATAAACACC

                            
      14694 TTTCCATACATAAACA
          1 TTTCCATACATAAACA

      14710 TCCAGTAACA


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   30  1.00

ACGTcount: A:0.42, C:0.29, G:0.02, T:0.27


Consensus pattern (18 bp):   
TTTCCATACATAAACACC

Found at i:16786 original size:13 final size:13

Alignment explanation


    Indices: 16768--16798  Score: 53
    Period size: 13  Copynumber: 2.4  Consensus size: 13

      16758 AATAACAAGC

                        *
      16768 AAAATCATTTACT
          1 AAAATCATTTACA

                         
      16781 AAAATCATTTACA
          1 AAAATCATTTACA

                 
      16794 AAAAT
          1 AAAAT

      16799 AATTAAAAGA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32


Consensus pattern (13 bp):   
AAAATCATTTACA
Done.