Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001425.1 Corchorus capsularis cultivar CVL-1 contig01425, 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: 7664
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:3134 original size:33 final size:33

Alignment explanation


    Indices: 3097--3169  Score: 105
    Period size: 31  Copynumber: 2.3  Consensus size: 33

       3087 TTAATTTCCT

                           *                *
       3097 AAATCATATAAGCTATAGAGAATCGCATTAAAG
          1 AAATCATATAAGCTACAGAGAATCGCATTAAAC

                                     *       
       3130 AAATC--ATAAGCTACAGAGAATCGTATTAAAC
          1 AAATCATATAAGCTACAGAGAATCGCATTAAAC

                     
       3161 AAATCATAT
          1 AAATCATAT

       3170 TACGATTTTG


Statistics
Matches: 35,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  31   28  0.80
  33    7  0.20

ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25


Consensus pattern (33 bp):   
AAATCATATAAGCTACAGAGAATCGCATTAAAC

Found at i:3561 original size:32 final size:32

Alignment explanation


    Indices: 3522--3594  Score: 110
    Period size: 32  Copynumber: 2.3  Consensus size: 32

       3512 CTTGAGTCGA

                      *                     
       3522 GTTCGGGTTGGATTTGGGTCAGATTAAATCGG
          1 GTTCGGGTTGAATTTGGGTCAGATTAAATCGG

            *                     *    *    
       3554 TTTCGGGTTGAATTTGGGTCAGGTTAATTCGG
          1 GTTCGGGTTGAATTTGGGTCAGATTAAATCGG

                     
       3586 GTTCGGGTT
          1 GTTCGGGTT

       3595 CTGTTTGGGT


Statistics
Matches: 36,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  32   36  1.00

ACGTcount: A:0.15, C:0.10, G:0.37, T:0.38


Consensus pattern (32 bp):   
GTTCGGGTTGAATTTGGGTCAGATTAAATCGG

Found at i:3602 original size:32 final size:32

Alignment explanation


    Indices: 3522--3604  Score: 94
    Period size: 32  Copynumber: 2.6  Consensus size: 32

       3512 CTTGAGTCGA

                     **                     
       3522 GTTCGGGTTGGATTTGGGTCAGATTAAATCGG
          1 GTTCGGGTTCAATTTGGGTCAGATTAAATCGG

            *        *            *    *    
       3554 TTTCGGGTTGAATTTGGGTCAGGTTAATTCGG
          1 GTTCGGGTTCAATTTGGGTCAGATTAAATCGG

                      **       
       3586 GTTCGGGTTCTGTTTGGGT
          1 GTTCGGGTTCAATTTGGGT

       3605 TTTAGCCAGA


Statistics
Matches: 43,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  32   43  1.00

ACGTcount: A:0.13, C:0.10, G:0.37, T:0.40


Consensus pattern (32 bp):   
GTTCGGGTTCAATTTGGGTCAGATTAAATCGG

Found at i:3797 original size:32 final size:32

Alignment explanation


    Indices: 3756--3865  Score: 193
    Period size: 32  Copynumber: 3.4  Consensus size: 32

       3746 TTTGGATTCA

                                            
       3756 GGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCG
          1 GGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCG

                                          * 
       3788 GGTTTTTTCGGGTTTGAGCTTTTTCGGGTTTG
          1 GGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCG

            * *                             
       3820 AGCTTTTTCGGGTTTGAGCTTTTTCGGGTTCG
          1 GGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCG

                          
       3852 GGTTTTTTCGGGTT
          1 GGTTTTTTCGGGTT

       3866 CGGGTTCAGA


Statistics
Matches: 72,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  32   72  1.00

ACGTcount: A:0.04, C:0.12, G:0.34, T:0.51


Consensus pattern (32 bp):   
GGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCG

Found at i:3871 original size:16 final size:16

Alignment explanation


    Indices: 3759--3865  Score: 160
    Period size: 16  Copynumber: 6.7  Consensus size: 16

       3749 GGATTCAGGT

                            
       3759 TTTTTCGGGTTTGAGC
          1 TTTTTCGGGTTTGAGC

                       * * *
       3775 TTTTTCGGGTTCGGGT
          1 TTTTTCGGGTTTGAGC

                            
       3791 TTTTTCGGGTTTGAGC
          1 TTTTTCGGGTTTGAGC

                            
       3807 TTTTTCGGGTTTGAGC
          1 TTTTTCGGGTTTGAGC

                            
       3823 TTTTTCGGGTTTGAGC
          1 TTTTTCGGGTTTGAGC

                       * * *
       3839 TTTTTCGGGTTCGGGT
          1 TTTTTCGGGTTTGAGC

                       
       3855 TTTTTCGGGTT
          1 TTTTTCGGGTT

       3866 CGGGTTCAGA


Statistics
Matches: 82,  Mismatches: 9, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  16   82  1.00

ACGTcount: A:0.04, C:0.12, G:0.33, T:0.51


Consensus pattern (16 bp):   
TTTTTCGGGTTTGAGC
Done.