Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023268.1 Corchorus olitorius cultivar O-4 contig23301, 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: 10557
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--27  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

                                                    
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

         28 GGCAAAAGGA


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

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:321 original size:3 final size:3

Alignment explanation


    Indices: 313--358  Score: 92
    Period size: 3  Copynumber: 15.3  Consensus size: 3

        303 GTTAATGGGC

                                                                         
        313 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

        359 GAAAATGGTC


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   43  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:2691 original size:12 final size:11

Alignment explanation


    Indices: 2668--2697  Score: 51
    Period size: 12  Copynumber: 2.6  Consensus size: 11

       2658 CACCAATACT

                       
       2668 CAAATTAACAA
          1 CAAATTAACAA

                        
       2679 CAAATTCAACAA
          1 CAAATT-AACAA

                   
       2691 CAAATTA
          1 CAAATTA

       2698 CTTACCCAAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  11    7  0.39
  12   11  0.61

ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20


Consensus pattern (11 bp):   
CAAATTAACAA

Found at i:5769 original size:11 final size:11

Alignment explanation


    Indices: 5753--5787  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       5743 CAGGGTTTGC

                       
       5753 TTTCTTTACTT
          1 TTTCTTTACTT

                   *   
       5764 TTTCTTTTCTT
          1 TTTCTTTACTT

               *       
       5775 TTTATTTACTT
          1 TTTCTTTACTT

              
       5786 TT
          1 TT

       5788 CTAAGTTTTA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  11   21  1.00

ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77


Consensus pattern (11 bp):   
TTTCTTTACTT
Done.