Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014397.1 Corchorus capsularis cultivar CVL-1 contig14418, 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: 11585
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27


Found at i:744 original size:30 final size:30

Alignment explanation


    Indices: 707--842  Score: 129
    Period size: 30  Copynumber: 4.6  Consensus size: 30

        697 TTGTCAAGAG

                             *            
        707 GAGCAGTGGGTTGAGCATCCTCCTCGGGAA
          1 GAGCAGTGGGTTGAGCACCCTCCTCGGGAA

            *              *      *       
        737 AAGCAGTGGGTTGAGGACCCTCGTC-GGAA
          1 GAGCAGTGGGTTGAGCACCCTCCTCGGGAA

                            *              *
        766 GGAGCAGTGGGTTGAGGACCCTCGC-CGGGAG
          1 -GAGCAGTGGGTTGAGCACCCTC-CTCGGGAA

                   *              *       
        797 GAGCAGTAGGTTGAGCACCCTCATC---AA
          1 GAGCAGTGGGTTGAGCACCCTCCTCGGGAA

             *      *          
        824 GGGCAGTGAGTTGAGCACC
          1 GAGCAGTGGGTTGAGCACC

        843 ATCAATGGGT


Statistics
Matches: 88,  Mismatches: 14, Indels: 11
        0.78            0.12        0.10

Matches are distributed among these distances:
  27   17  0.19
  29    4  0.05
  30   64  0.73
  31    3  0.03

ACGTcount: A:0.22, C:0.23, G:0.38, T:0.17


Consensus pattern (30 bp):   
GAGCAGTGGGTTGAGCACCCTCCTCGGGAA

Found at i:802 original size:60 final size:58

Alignment explanation


    Indices: 705--842  Score: 163
    Period size: 60  Copynumber: 2.4  Consensus size: 58

        695 TCTTGTCAAG

                               *                   *       *      *     
        705 AGGAGCAGTGGGTTGAGCATCCTCCTCGGGAAAAGCAGTGGGTTGAGGACCCTCGTCGGA
          1 AGGAGCAGTGGGTTGAGCACCCTCCTCGGGAAAAGCAGTAGGTTGAGCACCCTCATC--A

                             *              **                         
        765 AGGAGCAGTGGGTTGAGGACCCTCGC-CGGGAGGAGCAGTAGGTTGAGCACCCTCATCA
          1 AGGAGCAGTGGGTTGAGCACCCTC-CTCGGGAAAAGCAGTAGGTTGAGCACCCTCATCA

                      *          
        823 AGG-GCAGTGAGTTGAGCACC
          1 AGGAGCAGTGGGTTGAGCACC

        843 ATCAATGGGT


Statistics
Matches: 68,  Mismatches: 9, Indels: 5
        0.83            0.11        0.06

Matches are distributed among these distances:
  57   15  0.22
  58    4  0.06
  60   48  0.71
  61    1  0.01

ACGTcount: A:0.22, C:0.22, G:0.38, T:0.17


Consensus pattern (58 bp):   
AGGAGCAGTGGGTTGAGCACCCTCCTCGGGAAAAGCAGTAGGTTGAGCACCCTCATCA

Found at i:5057 original size:19 final size:19

Alignment explanation


    Indices: 5000--5059  Score: 52
    Period size: 19  Copynumber: 3.2  Consensus size: 19

       4990 TCTAGAAACA

                               
       5000 AATATCAAATATTCCTATT
          1 AATATCAAATATTCCTATT

                *   * *      *   
       5019 AATTTTACTACTATT--AATT
          1 AA-TAT-CAAATATTCCTATT

                               
       5038 AATATCAAATATTCCTATT
          1 AATATCAAATATTCCTATT

               
       5057 AAT
          1 AAT

       5060 TTTGCCATGA


Statistics
Matches: 29,  Mismatches: 8, Indels: 8
        0.64            0.18        0.18

Matches are distributed among these distances:
  17    6  0.21
  18    2  0.07
  19   13  0.45
  20    2  0.07
  21    6  0.21

ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45


Consensus pattern (19 bp):   
AATATCAAATATTCCTATT

Found at i:10061 original size:34 final size:34

Alignment explanation


    Indices: 10018--10085  Score: 127
    Period size: 34  Copynumber: 2.0  Consensus size: 34

      10008 TCTATATGAA

                                     *        
      10018 CAGAACTTTGAACAGTTTTTGCACAGTAAAAGGT
          1 CAGAACTTTGAACAGTTTTTGCACAATAAAAGGT

                                              
      10052 CAGAACTTTGAACAGTTTTTGCACAATAAAAGGT
          1 CAGAACTTTGAACAGTTTTTGCACAATAAAAGGT

      10086 GGGGATTGCT


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   33  1.00

ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29


Consensus pattern (34 bp):   
CAGAACTTTGAACAGTTTTTGCACAATAAAAGGT
Done.