Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015171.1 Corchorus capsularis cultivar CVL-1 contig15192, 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: 52127
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:9584 original size:6 final size:6

Alignment explanation


    Indices: 9573--9602  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       9563 GGTACTACTA

                                              
       9573 GAATAG GAATAG GAATAG GAATAG GAATAG
          1 GAATAG GAATAG GAATAG GAATAG GAATAG

       9603 CTACTTCTTC


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

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17


Consensus pattern (6 bp):   
GAATAG

Found at i:10569 original size:5 final size:5

Alignment explanation


    Indices: 10559--10593  Score: 70
    Period size: 5  Copynumber: 7.0  Consensus size: 5

      10549 CTCTTAATTC

                                                     
      10559 AAGCA AAGCA AAGCA AAGCA AAGCA AAGCA AAGCA
          1 AAGCA AAGCA AAGCA AAGCA AAGCA AAGCA AAGCA

      10594 CATGGTTGGC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   30  1.00

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


Consensus pattern (5 bp):   
AAGCA

Found at i:15775 original size:14 final size:15

Alignment explanation


    Indices: 15746--15784  Score: 53
    Period size: 14  Copynumber: 2.7  Consensus size: 15

      15736 TATATAATAA

                 *         
      15746 TATAGATTACTATTT
          1 TATAGTTTACTATTT

                           
      15761 TATAGTTTA-TATTT
          1 TATAGTTTACTATTT

                *     
      15775 TATAATTTAC
          1 TATAGTTTAC

      15785 AGGTAATAGG


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  14   13  0.62
  15    8  0.38

ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56


Consensus pattern (15 bp):   
TATAGTTTACTATTT

Found at i:26484 original size:21 final size:17

Alignment explanation


    Indices: 26444--26478  Score: 61
    Period size: 18  Copynumber: 2.0  Consensus size: 17

      26434 ATTTAAAACA

                             
      26444 TTAACTAATAATGTTGC
          1 TTAACTAATAATGTTGC

                              
      26461 TTAATCTAATAATGTTGC
          1 TTAA-CTAATAATGTTGC

      26479 AGCTTACCTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17    4  0.24
  18   13  0.76

ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43


Consensus pattern (17 bp):   
TTAACTAATAATGTTGC

Found at i:26662 original size:2 final size:2

Alignment explanation


    Indices: 26655--26687  Score: 57
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      26645 AACCTAATAC

                                                            
      26655 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT

      26688 CTAATGATTC


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

Matches are distributed among these distances:
   2   28  0.93
   3    2  0.07

ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:35668 original size:2 final size:2

Alignment explanation


    Indices: 35661--35697  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      35651 AAATTTTTGT

                                                                   
      35661 TA TA TA TA TA 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 TA TA TA TA TA T

      35698 CGATTAATGG


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:45539 original size:30 final size:32

Alignment explanation


    Indices: 45505--45564  Score: 79
    Period size: 33  Copynumber: 1.9  Consensus size: 32

      45495 GCTCAAAACC

                                *           
      45505 ACCACCT-ACA-GGCCGAAACCCTCCACCAGA
          1 ACCACCTCACATGGCCGAAAACCTCCACCAGA

                    *                     
      45535 ACCACCTCCCATTGGCCGAAAACCTCCACC
          1 ACCACCTCACA-TGGCCGAAAACCTCCACC

      45565 TCCTGCTGCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  30    7  0.28
  31    2  0.08
  33   16  0.64

ACGTcount: A:0.30, C:0.48, G:0.12, T:0.10


Consensus pattern (32 bp):   
ACCACCTCACATGGCCGAAAACCTCCACCAGA

Found at i:46685 original size:44 final size:42

Alignment explanation


    Indices: 46636--46718  Score: 112
    Period size: 44  Copynumber: 1.9  Consensus size: 42

      46626 TTAAGGGGTA

                                                        
      46636 AAAGGCAAAATCCTTGATTGAAAGCAACAAACAAAAGGTGTCAG
          1 AAAGGCAAAATCCTTGATTG-AAGCAACAAA-AAAAGGTGTCAG

                       **            *    *        
      46680 AAAGGCAAAATGTTTGATTGAAGCAGCAAAGAAAGGTGT
          1 AAAGGCAAAATCCTTGATTGAAGCAACAAAAAAAGGTGT

      46719 TGGAACTGGA


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  42    8  0.23
  43    9  0.26
  44   18  0.51

ACGTcount: A:0.46, C:0.12, G:0.24, T:0.18


Consensus pattern (42 bp):   
AAAGGCAAAATCCTTGATTGAAGCAACAAAAAAAGGTGTCAG
Done.