Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016122.1 Corchorus capsularis cultivar CVL-1 contig16143, 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: 5574
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35


Found at i:1928 original size:32 final size:32

Alignment explanation


    Indices: 1862--1937  Score: 89
    Period size: 32  Copynumber: 2.4  Consensus size: 32

       1852 AATGATCAAA

                                  **     *  
       1862 ACGCCACTATTTAACGGCGTCTTTTAAATTAG
          1 ACGCCACTATTTAACGGCGTCTAATAAATCAG

                         *           * *    
       1894 ACGCCACTATTTAGCGGCGTCTAATCACTCAG
          1 ACGCCACTATTTAACGGCGTCTAATAAATCAG

                 *      
       1926 ACGCCGCTATTT
          1 ACGCCACTATTT

       1938 GGTGGAGTCT


Statistics
Matches: 37,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  32   37  1.00

ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30


Consensus pattern (32 bp):   
ACGCCACTATTTAACGGCGTCTAATAAATCAG

Found at i:2715 original size:13 final size:13

Alignment explanation


    Indices: 2697--2721  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2687 GGTCAGCAGA

                         
       2697 TTCCTTTTCTCCC
          1 TTCCTTTTCTCCC

                        
       2710 TTCCTTTTCTCC
          1 TTCCTTTTCTCC

       2722 TGATGGTTTC


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:0.00, C:0.44, G:0.00, T:0.56


Consensus pattern (13 bp):   
TTCCTTTTCTCCC

Found at i:3255 original size:14 final size:14

Alignment explanation


    Indices: 3238--3265  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       3228 TTAGTGTATC

                          
       3238 TGTTTTAGATTTGT
          1 TGTTTTAGATTTGT

                          
       3252 TGTTTTAGATTTGT
          1 TGTTTTAGATTTGT

       3266 GAATGATTCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.14, C:0.00, G:0.21, T:0.64


Consensus pattern (14 bp):   
TGTTTTAGATTTGT

Found at i:4291 original size:27 final size:27

Alignment explanation


    Indices: 4255--4398  Score: 243
    Period size: 27  Copynumber: 5.3  Consensus size: 27

       4245 GTCTTCTCTC

                           **          
       4255 CCCACTTCGACCCCAAAAGTGGATCCT
          1 CCCACTTCGACCCCAGCAGTGGATCCT

                                       
       4282 CCCACTTCGACCCCAGCAGTGGATCCT
          1 CCCACTTCGACCCCAGCAGTGGATCCT

                              *        
       4309 CCCACTTCGACCCCAGCAATGGATCCT
          1 CCCACTTCGACCCCAGCAGTGGATCCT

              *      *                 
       4336 CCTACTTCGGCCCCAGCAGTGGATCCT
          1 CCCACTTCGACCCCAGCAGTGGATCCT

                                       
       4363 CCCACTTCGACCCCAGCAGTGGATCCT
          1 CCCACTTCGACCCCAGCAGTGGATCCT

                     
       4390 CCCACTTCG
          1 CCCACTTCG

       4399 CCTATGGTGG


Statistics
Matches: 109,  Mismatches: 8, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  27  109  1.00

ACGTcount: A:0.19, C:0.44, G:0.17, T:0.19


Consensus pattern (27 bp):   
CCCACTTCGACCCCAGCAGTGGATCCT

Done.