Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013710.1 Corchorus capsularis cultivar CVL-1 contig13731, 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: 28388
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:12964 original size:2 final size:2

Alignment explanation


    Indices: 12957--13001  Score: 90
    Period size: 2  Copynumber: 22.5  Consensus size: 2

      12947 TTGAGAGTGG

                                                                          
      12957 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT

                
      12999 AT A
          1 AT A

      13002 GACATGTTGC


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

Matches are distributed among these distances:
   2   43  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:13756 original size:25 final size:25

Alignment explanation


    Indices: 13722--13794  Score: 112
    Period size: 25  Copynumber: 2.9  Consensus size: 25

      13712 TTTCTTTAAC

                          *          
      13722 TTTCTTAAACTTGAAAAGCCCATAA
          1 TTTCTTAAACTTGAGAAGCCCATAA

                                     
      13747 TTTCTTAAACTTGAGAAGCCCA-AA
          1 TTTCTTAAACTTGAGAAGCCCATAA

             *                      
      13771 TATCTTAATACTTGAGAAGCCCAT
          1 TTTCTTAA-ACTTGAGAAGCCCAT

      13795 TTTTTCTTTT


Statistics
Matches: 44,  Mismatches: 2, Indels: 3
        0.90            0.04        0.06

Matches are distributed among these distances:
  24    9  0.20
  25   35  0.80

ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32


Consensus pattern (25 bp):   
TTTCTTAAACTTGAGAAGCCCATAA

Found at i:22339 original size:12 final size:12

Alignment explanation


    Indices: 22322--22347  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      22312 TTTTCATAAT

                        
      22322 TTAGTGACTAAA
          1 TTAGTGACTAAA

                        
      22334 TTAGTGACTAAA
          1 TTAGTGACTAAA

              
      22346 TT
          1 TT

      22348 TTTTTTTCTC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38


Consensus pattern (12 bp):   
TTAGTGACTAAA

Found at i:22472 original size:25 final size:25

Alignment explanation


    Indices: 22439--22495  Score: 107
    Period size: 25  Copynumber: 2.3  Consensus size: 25

      22429 ATCAATGGAT

                                     
      22439 TATA-ATTGCATCAATTTTCAATTC
          1 TATAGATTGCATCAATTTTCAATTC

                                     
      22463 TATAGATTGCATCAATTTTCAATTC
          1 TATAGATTGCATCAATTTTCAATTC

                    
      22488 TATAGATT
          1 TATAGATT

      22496 ACCATGACTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  24    4  0.12
  25   28  0.88

ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46


Consensus pattern (25 bp):   
TATAGATTGCATCAATTTTCAATTC

Found at i:26414 original size:2 final size:2

Alignment explanation


    Indices: 26407--26440  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      26397 AATTAATCCA

                                                              
      26407 AT AT AT AT 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 AT AT AT AT

      26441 GCTTTCAGAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:27895 original size:2 final size:2

Alignment explanation


    Indices: 27878--27920  Score: 65
    Period size: 2  Copynumber: 23.0  Consensus size: 2

      27868 GTGCATTCAA

                                                                          
      27878 AT AT A- AT AT AT A- AT AT AT A- AT AT 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 AT AT AT AT AT

                 
      27917 AT AT
          1 AT AT

      27921 GTATGTGTGG


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


Consensus pattern (2 bp):   
AT

Found at i:27897 original size:14 final size:15

Alignment explanation


    Indices: 27878--27920  Score: 72
    Period size: 14  Copynumber: 3.0  Consensus size: 15

      27868 GTGCATTCAA

                           
      27878 ATATAATATATA-AT
          1 ATATAATATATATAT

                           
      27892 ATATAATATATATAT
          1 ATATAATATATATAT

                           
      27907 ATAT-ATATATATAT
          1 ATATAATATATATAT

      27921 GTATGTGTGG


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

Matches are distributed among these distances:
  14   22  0.79
  15    6  0.21

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


Consensus pattern (15 bp):   
ATATAATATATATAT

Done.