Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008034.1 Corchorus capsularis cultivar CVL-1 contig08055, 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: 17380
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33


Found at i:1583 original size:26 final size:26

Alignment explanation


    Indices: 1546--1607  Score: 115
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       1536 GCGATATTTT

                                       
       1546 TTTTCATTTGCTTTTCAGTTTGAGACC
          1 TTTT-ATTTGCTTTTCAGTTTGAGACC

                                      
       1573 TTTTATTTGCTTTTCAGTTTGAGACC
          1 TTTTATTTGCTTTTCAGTTTGAGACC

                     
       1599 TTTTATTTG
          1 TTTTATTTG

       1608 GGCCTTTTTT


Statistics
Matches: 35,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  26   31  0.89
  27    4  0.11

ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56


Consensus pattern (26 bp):   
TTTTATTTGCTTTTCAGTTTGAGACC

Found at i:9887 original size:10 final size:9

Alignment explanation


    Indices: 9873--9898  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

       9863 TAATTTTCTG

                     
       9873 ATTTTTTCC
          1 ATTTTTTCC

                     
       9882 ATTTTTTCC
          1 ATTTTTTCC

                    
       9891 ATTTTTTC
          1 ATTTTTTC

       9899 TTTTCCTTCT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69


Consensus pattern (9 bp):   
ATTTTTTCC

Found at i:15637 original size:22 final size:23

Alignment explanation


    Indices: 15612--15671  Score: 79
    Period size: 22  Copynumber: 2.7  Consensus size: 23

      15602 TGATCTACAT

                                   
      15612 ACTATGAAATTTTGA-AAACTAA
          1 ACTATGAAATTTTGATAAACTAA

                              *  **
      15634 ACTATGAAATTTTGATAACCTTC
          1 ACTATGAAATTTTGATAAACTAA

                            
      15657 A-TATGAAATTTTGAT
          1 ACTATGAAATTTTGAT

      15672 TACTCCATAA


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  22   29  0.85
  23    5  0.15

ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38


Consensus pattern (23 bp):   
ACTATGAAATTTTGATAAACTAA

Found at i:15802 original size:22 final size:22

Alignment explanation


    Indices: 15777--15830  Score: 90
    Period size: 22  Copynumber: 2.5  Consensus size: 22

      15767 AATCACATTT

                              *   
      15777 TGAAATTTTGATAACCTCTTTA
          1 TGAAATTTTGATAACCTCGTTA

                                  
      15799 TGAAATTTTGATAACCTCGTTA
          1 TGAAATTTTGATAACCTCGTTA

             *        
      15821 TAAAATTTTG
          1 TGAAATTTTG

      15831 TTGACCCCTC


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  22   30  1.00

ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44


Consensus pattern (22 bp):   
TGAAATTTTGATAACCTCGTTA
Done.