Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010056.1 Corchorus capsularis cultivar CVL-1 contig10077, 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: 13431
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:5084 original size:2 final size:2

Alignment explanation


    Indices: 5079--5121  Score: 65
    Period size: 2  Copynumber: 23.0  Consensus size: 2

       5069 TGTGTGTGTG

                                                                          
       5079 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                 
       5118 TA TA
          1 TA TA

       5122 CATTAAAACT


Statistics
Matches: 38,  Mismatches: 0, Indels: 6
        0.86            0.00        0.14

Matches are distributed among these distances:
   1    3  0.08
   2   35  0.92

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:5126 original size:12 final size:13

Alignment explanation


    Indices: 5079--5126  Score: 64
    Period size: 12  Copynumber: 3.8  Consensus size: 13

       5069 TGTGTGTGTG

                     *   
       5079 TATATATATAATA
          1 TATATATATTATA

                         
       5092 TATATATA-TATA
          1 TATATATATTATA

                         
       5104 TATATATATTAT-
          1 TATATATATTATA

                  *    
       5116 TATATACATTA
          1 TATATATATTA

       5127 AAACTTGAAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 3
        0.86            0.05        0.08

Matches are distributed among these distances:
  12   21  0.66
  13   11  0.34

ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50


Consensus pattern (13 bp):   
TATATATATTATA

Found at i:6960 original size:2 final size:2

Alignment explanation


    Indices: 6953--6978  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       6943 TTTTTATTTA

                                                  
       6953 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       6979 TAATTGGTTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:12978 original size:19 final size:20

Alignment explanation


    Indices: 12940--12981  Score: 59
    Period size: 19  Copynumber: 2.1  Consensus size: 20

      12930 ATGTTTGGCA

                          **    
      12940 TTGTTGCCATTTTTGTTTTT
          1 TTGTTGCCATTTTTCATTTT

                                
      12960 TTGTTGCCA-TTTTCATTTT
          1 TTGTTGCCATTTTTCATTTT

               
      12979 TTG
          1 TTG

      12982 AAAACAAACA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  19   11  0.55
  20    9  0.45

ACGTcount: A:0.07, C:0.12, G:0.14, T:0.67


Consensus pattern (20 bp):   
TTGTTGCCATTTTTCATTTT

Found at i:12978 original size:20 final size:20

Alignment explanation


    Indices: 12940--12980  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      12930 ATGTTTGGCA

                         **     
      12940 TTGTTGCCATTTTTGTTTTT
          1 TTGTTGCCATTTTCATTTTT

                                
      12960 TTGTTGCCATTTTCATTTTT
          1 TTGTTGCCATTTTCATTTTT

             
      12980 T
          1 T

      12981 GAAAACAAAC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.07, C:0.12, G:0.12, T:0.68


Consensus pattern (20 bp):   
TTGTTGCCATTTTCATTTTT
Done.