Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023145.1 Corchorus olitorius cultivar O-4 contig23178, 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: 20533
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:10360 original size:21 final size:21

Alignment explanation


    Indices: 10321--10360  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      10311 AGGAGATGCC

                        *        
      10321 AAAGATGCCATTTGATCCATT
          1 AAAGATGCCATTAGATCCATT

                          *    
      10342 AAAGATGCCATTAGGTCCA
          1 AAAGATGCCATTAGATCCA

      10361 ATGACAAGAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28


Consensus pattern (21 bp):   
AAAGATGCCATTAGATCCATT

Found at i:11665 original size:53 final size:51

Alignment explanation


    Indices: 11567--11768  Score: 271
    Period size: 52  Copynumber: 3.9  Consensus size: 51

      11557 ATTGAAAACT

                    *                 *             *            
      11567 AAAACCTGGTGGGAACTTTCCCAATTCGAAAAAGAGCCTACTTGAATACTTTG
          1 AAAA-CTGATGGGAACTTTCCCAATTTGAAAAAGAG-CTAATTGAATACTTTG

                    *                                            
      11620 AAAACTGACGGGAACTTTCCCAATTTGAAAAAAGAGCTAGATTGAATACTTTG
          1 AAAACTGATGGGAACTTTCCCAATTTG-AAAAAGAGCTA-ATTGAATACTTTG

                                  * *                            
      11673 AAAACT-AGTGGGAACTTTCCCGACTTGAAAAAGAGCTAAATTGAATACTTTG
          1 AAAACTGA-TGGGAACTTTCCCAATTTGAAAAAGAGCT-AATTGAATACTTTG

                                 *                 *    
      11725 AAAACTGATGGGAACTTTCCCGATTTGAAAAAGAGCTAAATGAA
          1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAATTGAA

      11769 ATTCTTTTTT


Statistics
Matches: 135,  Mismatches: 9, Indels: 12
        0.87            0.06        0.08

Matches are distributed among these distances:
  51    6  0.04
  52   81  0.60
  53   48  0.36

ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26


Consensus pattern (51 bp):   
AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAATTGAATACTTTG

Found at i:14188 original size:16 final size:16

Alignment explanation


    Indices: 14167--14206  Score: 71
    Period size: 16  Copynumber: 2.4  Consensus size: 16

      14157 TTGTGCATTA

                            
      14167 ATGCCTTTAAAATGTG
          1 ATGCCTTTAAAATGTG

                            
      14183 ATGCCTTTAAAATGTG
          1 ATGCCTTTAAAATGTG

                    
      14199 ATGGCCTT
          1 AT-GCCTT

      14207 GATTCACCTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  16   18  0.78
  17    5  0.22

ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38


Consensus pattern (16 bp):   
ATGCCTTTAAAATGTG

Found at i:15987 original size:36 final size:37

Alignment explanation


    Indices: 15920--15991  Score: 110
    Period size: 36  Copynumber: 2.0  Consensus size: 37

      15910 GAAAGAGTTC

                                      *          
      15920 CAAGCCAATTGGTTCGAAAATGGAAGGGAAAGTAGCT
          1 CAAGCCAATTGGTTCGAAAATGGAAGAGAAAGTAGCT

                   *          *                 
      15957 CAAGCCAGTTGGTTCG-AGATGGAAGAGAAAGTAGC
          1 CAAGCCAATTGGTTCGAAAATGGAAGAGAAAGTAGC

      15992 CTTATAAATG


Statistics
Matches: 32,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  36   17  0.53
  37   15  0.47

ACGTcount: A:0.36, C:0.14, G:0.32, T:0.18


Consensus pattern (37 bp):   
CAAGCCAATTGGTTCGAAAATGGAAGAGAAAGTAGCT

Found at i:17392 original size:17 final size:17

Alignment explanation


    Indices: 17370--17405  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      17360 ATACAAAGAG

                             
      17370 CTATCTAGTATAACAAA
          1 CTATCTAGTATAACAAA

                  *  *       
      17387 CTATCTGGTGTAACAAA
          1 CTATCTAGTATAACAAA

              
      17404 CT
          1 CT

      17406 TTACAAATTA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31


Consensus pattern (17 bp):   
CTATCTAGTATAACAAA

Found at i:18041 original size:17 final size:17

Alignment explanation


    Indices: 18019--18054  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      18009 ATACAAAGAG

                             
      18019 CTATCTAGTATAACAAA
          1 CTATCTAGTATAACAAA

                  *  *       
      18036 CTATCTGGTGTAACAAA
          1 CTATCTAGTATAACAAA

              
      18053 CT
          1 CT

      18055 TTACAAATCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31


Consensus pattern (17 bp):   
CTATCTAGTATAACAAA
Done.