Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008449.1 Corchorus olitorius cultivar O-4 contig08476, 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, 748

Length: 1248
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27


Found at i:490 original size:10 final size:10

Alignment explanation


    Indices: 475--511  Score: 51
    Period size: 10  Copynumber: 3.9  Consensus size: 10

        465 CTAGCCAGCA

                      
        475 CGCGGGCCAG
          1 CGCGGGCCAG

                      
        485 CGCGGGCCAG
          1 CGCGGGCCAG

                      
        495 CGC-GGCCA-
          1 CGCGGGCCAG

                *    
        503 CGCGTGCCA
          1 CGCGGGCCA

        512 ACCAGTACGC


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
   8    3  0.12
   9    9  0.36
  10   13  0.52

ACGTcount: A:0.11, C:0.43, G:0.43, T:0.03


Consensus pattern (10 bp):   
CGCGGGCCAG

Found at i:523 original size:34 final size:35

Alignment explanation


    Indices: 485--578  Score: 138
    Period size: 35  Copynumber: 2.7  Consensus size: 35

        475 CGCGGGCCAG

                                              * 
        485 CGCGGGCCAGCGCGG-CCACGCGTGCCAA-CCAGTA
          1 CGCGGGCCAGCGCGGCCCA-GCGTGCCAAGCCAGCA

                                 *             
        519 CGCGGGCCAGCGCGGCCCAGCATGCCAAGCCAGCA
          1 CGCGGGCCAGCGCGGCCCAGCGTGCCAAGCCAGCA

                       *             
        554 CGCGGGCCAGCACGGCCCAGCGTGC
          1 CGCGGGCCAGCGCGGCCCAGCGTGC

        579 TAGGCTTGGT


Statistics
Matches: 54,  Mismatches: 4, Indels: 3
        0.89            0.07        0.05

Matches are distributed among these distances:
  34   23  0.43
  35   31  0.57

ACGTcount: A:0.17, C:0.43, G:0.36, T:0.04


Consensus pattern (35 bp):   
CGCGGGCCAGCGCGGCCCAGCGTGCCAAGCCAGCA

Found at i:665 original size:16 final size:16

Alignment explanation


    Indices: 641--719  Score: 65
    Period size: 16  Copynumber: 4.9  Consensus size: 16

        631 AAATAAATCA

                     *       
        641 AAAATAAAATAGAAAGG
          1 AAAA-AAAAGAGAAAGG

                             
        658 AAAAAAAAGA-ATAAGG
          1 AAAAAAAAGAGA-AAGG

                *            
        674 AAGAGAAAA-AGAAAGG
          1 AA-AAAAAAGAGAAAGG

                      *      
        690 AAAAAAAA-ATATAAGG
          1 AAAAAAAAGAGA-AAGG

                *         
        706 AAAATAAAGAGAAA
          1 AAAAAAAAGAGAAA

        720 TTTGGAAATA


Statistics
Matches: 51,  Mismatches: 6, Indels: 11
        0.75            0.09        0.16

Matches are distributed among these distances:
  15    8  0.16
  16   31  0.61
  17   12  0.24

ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08


Consensus pattern (16 bp):   
AAAAAAAAGAGAAAGG

Found at i:719 original size:32 final size:32

Alignment explanation


    Indices: 641--719  Score: 106
    Period size: 32  Copynumber: 2.4  Consensus size: 32

        631 AAATAAATCA

                                             
        641 AAAATAAAATAGAAAGGAAAAAAAAGAATAAGG
          1 AAAATAAAA-AGAAAGGAAAAAAAAGAATAAGG

              * *                            
        674 AAGAGAAAAAGAAAGGAAAAAAAA-ATATAAGG
          1 AAAATAAAAAGAAAGGAAAAAAAAGA-ATAAGG

                    *     
        706 AAAATAAAGAGAAA
          1 AAAATAAAAAGAAA

        720 TTTGGAAATA


Statistics
Matches: 40,  Mismatches: 5, Indels: 3
        0.83            0.10        0.06

Matches are distributed among these distances:
  31    1  0.03
  32   32  0.80
  33    7  0.17

ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08


Consensus pattern (32 bp):   
AAAATAAAAAGAAAGGAAAAAAAAGAATAAGG
Done.