Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008851.1 Corchorus capsularis cultivar CVL-1 contig08872, 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: 3969
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35


Found at i:39 original size:13 final size:13

Alignment explanation


    Indices: 21--45  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

         11 CTCTTCCTTC

                         
         21 CTTTTCTCCTTTA
          1 CTTTTCTCCTTTA

                        
         34 CTTTTCTCCTTT
          1 CTTTTCTCCTTT

         46 CCTTCTCATT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.04, C:0.32, G:0.00, T:0.64


Consensus pattern (13 bp):   
CTTTTCTCCTTTA

Found at i:1329 original size:1 final size:1

Alignment explanation


    Indices: 1323--1348  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       1313 TTGTTGGTGG

                                      
       1323 TTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

       1349 ACAGTTGCAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:1784 original size:54 final size:54

Alignment explanation


    Indices: 1718--1861  Score: 182
    Period size: 54  Copynumber: 2.7  Consensus size: 54

       1708 TCCGGCTCTC

                *           *                   ****               
       1718 CCCATTTCGACCCCAGAAGTGGATCCTCCAACTGT-TTTTCCAACAGTGGATCCT
          1 CCCACTTCGACCCCAGCAGTGGATCCTCCAACT-TCGACCCCAACAGTGGATCCT

                                         *            **          
       1772 CCCACTTCGACCCCAGCAGTGGATCCTCCCACTTCGACCCCAGTAGTGGATCCT
          1 CCCACTTCGACCCCAGCAGTGGATCCTCCAACTTCGACCCCAACAGTGGATCCT

                                         *      
       1826 CCCACTTCGACCCCAGCAGTGGATCCTCCCACTTCG
          1 CCCACTTCGACCCCAGCAGTGGATCCTCCAACTTCG

       1862 CCTCGGGTCG


Statistics
Matches: 80,  Mismatches: 9, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  53    1  0.01
  54   79  0.99

ACGTcount: A:0.19, C:0.40, G:0.17, T:0.23


Consensus pattern (54 bp):   
CCCACTTCGACCCCAGCAGTGGATCCTCCAACTTCGACCCCAACAGTGGATCCT

Found at i:1791 original size:27 final size:27

Alignment explanation


    Indices: 1761--1861  Score: 193
    Period size: 27  Copynumber: 3.7  Consensus size: 27

       1751 GTTTTTCCAA

                                       
       1761 CAGTGGATCCTCCCACTTCGACCCCAG
          1 CAGTGGATCCTCCCACTTCGACCCCAG

                                       
       1788 CAGTGGATCCTCCCACTTCGACCCCAG
          1 CAGTGGATCCTCCCACTTCGACCCCAG

            *                          
       1815 TAGTGGATCCTCCCACTTCGACCCCAG
          1 CAGTGGATCCTCCCACTTCGACCCCAG

                                
       1842 CAGTGGATCCTCCCACTTCG
          1 CAGTGGATCCTCCCACTTCG

       1862 CCTCGGGTCG


Statistics
Matches: 72,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   72  1.00

ACGTcount: A:0.18, C:0.43, G:0.19, T:0.21


Consensus pattern (27 bp):   
CAGTGGATCCTCCCACTTCGACCCCAG
Done.