Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012393.1 Corchorus capsularis cultivar CVL-1 contig12414, 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: 16260
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34


Found at i:12300 original size:2 final size:2

Alignment explanation


    Indices: 12295--12358  Score: 85
    Period size: 2  Copynumber: 31.5  Consensus size: 2

      12285 AAAGACATGC

                                                            * *             
      12295 TA TA TA TGA TA TA TA TA TA TA TA TA TA T- TCA TC CA TA TA TA TA
          1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA

                                           
      12338 TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA T

      12359 CTTACAAGTG


Statistics
Matches: 55,  Mismatches: 4, Indels: 6
        0.85            0.06        0.09

Matches are distributed among these distances:
   1    1  0.02
   2   51  0.93
   3    3  0.05

ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:13796 original size:21 final size:21

Alignment explanation


    Indices: 13758--13797  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      13748 CTGTTTAGCA

                       *         
      13758 ACTGTACAGATTAAATTATGT
          1 ACTGTACAGATGAAATTATGT

                  *      *     
      13779 ACTGTATAGATGAGATTAT
          1 ACTGTACAGATGAAATTAT

      13798 TAGAGCAGCT


Statistics
Matches: 16,  Mismatches: 3, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   16  1.00

ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38


Consensus pattern (21 bp):   
ACTGTACAGATGAAATTATGT

Found at i:14782 original size:5 final size:5

Alignment explanation


    Indices: 14772--14797  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

      14762 TAAAAAAAAC

                                           
      14772 CTTAT CTTAT CTTAT CTTAT CTTAT C
          1 CTTAT CTTAT CTTAT CTTAT CTTAT C

      14798 ATTTTTCAAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58


Consensus pattern (5 bp):   
CTTAT

Found at i:15732 original size:2 final size:2

Alignment explanation


    Indices: 15725--15756  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      15715 TATTTACCAA

                                  *                        
      15725 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      15757 GCATGTGTGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:16220 original size:2 final size:2

Alignment explanation


    Indices: 16208--16245  Score: 69
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      16198 TTCCCTTTGC

                                                                      
      16208 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      16246 GTCGTCCCGA


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   34  0.97

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.