Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006550.1 Corchorus capsularis cultivar CVL-1 contig06571, 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: 23420
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31


Found at i:2870 original size:21 final size:21

Alignment explanation


    Indices: 2846--2891  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       2836 CCAGGGCACA

                            *  * 
       2846 TGGGTGCCCAAGCAAATCGGC
          1 TGGGTGCCCAAGCAAAGCGCC

                   *  *          
       2867 TGGGTGCGCAGGCAAAGCGCC
          1 TGGGTGCCCAAGCAAAGCGCC

                
       2888 TGGG
          1 TGGG

       2892 CGCACAGCCA


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.20, C:0.26, G:0.41, T:0.13


Consensus pattern (21 bp):   
TGGGTGCCCAAGCAAAGCGCC

Found at i:8100 original size:21 final size:21

Alignment explanation


    Indices: 8074--8122  Score: 71
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       8064 GCGCTGGGCG

                          *     *
       8074 CCCATGTGGTTTGCTTAGCGC
          1 CCCATGTGGTTTGCCTAGCGA

                            *    
       8095 CCCATGTGGTTTGCCTCGCGA
          1 CCCATGTGGTTTGCCTAGCGA

                   
       8116 CCCATGT
          1 CCCATGT

       8123 ACTCTAGTGC


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.10, C:0.33, G:0.27, T:0.31


Consensus pattern (21 bp):   
CCCATGTGGTTTGCCTAGCGA

Found at i:15062 original size:2 final size:2

Alignment explanation


    Indices: 15049--15110  Score: 58
    Period size: 2  Copynumber: 32.5  Consensus size: 2

      15039 ATACAATCTT

                      *                          *    *      *        *   
      15049 TA TA TA TT TA TA TA TA TA TA TA TA TT TA GA -A TT TA -A TT TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                              
      15089 TA -A TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA T

      15111 TAATACTAAA


Statistics
Matches: 48,  Mismatches: 9, Indels: 6
        0.76            0.14        0.10

Matches are distributed among these distances:
   1    3  0.06
   2   45  0.94

ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:16405 original size:20 final size:21

Alignment explanation


    Indices: 16380--16432  Score: 72
    Period size: 21  Copynumber: 2.6  Consensus size: 21

      16370 ACTAGCGCTG

                               * 
      16380 GGCG-CCCATGTGGTTTGCTT
          1 GGCGACCCATGTGGTTTGCCT

                *                
      16400 GGCGCCCCATGTGGTTTGCCT
          1 GGCGACCCATGTGGTTTGCCT

            *           
      16421 CGCGACCCATGT
          1 GGCGACCCATGT

      16433 ACTCCAGTGC


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  20    4  0.14
  21   25  0.86

ACGTcount: A:0.08, C:0.32, G:0.32, T:0.28


Consensus pattern (21 bp):   
GGCGACCCATGTGGTTTGCCT

Done.