Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003660.1 Corchorus capsularis cultivar CVL-1 contig03668, 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: 6064
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:94 original size:2 final size:2

Alignment explanation


    Indices: 89--128  Score: 64
    Period size: 2  Copynumber: 20.0  Consensus size: 2

         79 ATACTCCGTA

                                                                        
         89 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT ACT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT

        129 TAATAAAGAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   1    1  0.03
   2   33  0.92
   3    2  0.06

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


Consensus pattern (2 bp):   
AT

Found at i:2559 original size:40 final size:39

Alignment explanation


    Indices: 2515--2638  Score: 196
    Period size: 40  Copynumber: 3.2  Consensus size: 39

       2505 TACCCAATAA

                                          *         
       2515 TCAAAGTCCCTAAACACATATAACACAAGGACAATTTCTC
          1 TCAAAGTCCCTAAACACATATAACACAAGGGCAA-TTCTC

                                                    
       2555 TCAAAGTCCCTAAACACATATAACACAAGGGCAATCTCTC
          1 TCAAAGTCCCTAAACACATATAACACAAGGGCAAT-TCTC

                    *          *                   
       2595 TCAAAGTCTCTAAACACATGTAACACAAGGGCAA-TCTC
          1 TCAAAGTCCCTAAACACATATAACACAAGGGCAATTCTC

                  
       2633 TCAAAG
          1 TCAAAG

       2639 GTGATAAAAC


Statistics
Matches: 80,  Mismatches: 3, Indels: 4
        0.92            0.03        0.05

Matches are distributed among these distances:
  38   10  0.12
  39    1  0.01
  40   69  0.86

ACGTcount: A:0.41, C:0.27, G:0.10, T:0.21


Consensus pattern (39 bp):   
TCAAAGTCCCTAAACACATATAACACAAGGGCAATTCTC

Found at i:5797 original size:2 final size:2

Alignment explanation


    Indices: 5790--5823  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       5780 AATCGTTTCA

                                              *               
       5790 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5824 TACTAGTTTT


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

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Done.