Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_D_gene_10034583

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, 640

Length: 1068
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18


Found at i:602 original size:18 final size:18

Alignment explanation


    Indices: 575--626  Score: 59
    Period size: 18  Copynumber: 2.9  Consensus size: 18

        565 GTTCCCCCTA

                 *    *     * 
        575 AGAAGGAAGATGCCGGTG
          1 AGAAGAAAGACGCCGGAG

                        *     
        593 AGAAGAAAGACGGCGGAG
          1 AGAAGAAAGACGCCGGAG

                   *        
        611 AGAAGAATGACGCCGG
          1 AGAAGAAAGACGCCGG

        627 CGGTGATAAA


Statistics
Matches: 28,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  18   28  1.00

ACGTcount: A:0.38, C:0.13, G:0.42, T:0.06


Consensus pattern (18 bp):   
AGAAGAAAGACGCCGGAG

Found at i:723 original size:39 final size:41

Alignment explanation


    Indices: 670--794  Score: 154
    Period size: 39  Copynumber: 3.1  Consensus size: 41

        660 TGCTGCAGGC

                            *           *             
        670 GGCGGCGGGAAGAAGGGAGGAGGA-G-GTGGAG-AGAAGGAA
          1 GGCGGC-GGAAGAAGGAAGGAGGAGGCGGGGAGAAGAAGGAA

                                                      
        709 GGCGGCGAGAAGAAGGAAGGAGGAGGCGGGGAGAAGAAGGAA
          1 GGCGGCG-GAAGAAGGAAGGAGGAGGCGGGGAGAAGAAGGAA

                                                  *   
        751 GGCGGCGGAGAGAA-GAAGGA--AGGCGGGGAGAAGAAAGAA
          1 GGCGGCGGA-AGAAGGAAGGAGGAGGCGGGGAGAAGAAGGAA

                 
        790 GGCGG
          1 GGCGG

        795 TGGTGAAGCC


Statistics
Matches: 78,  Mismatches: 3, Indels: 10
        0.86            0.03        0.11

Matches are distributed among these distances:
  38    1  0.01
  39   44  0.56
  40    1  0.01
  41   13  0.17
  42   19  0.24

ACGTcount: A:0.36, C:0.07, G:0.56, T:0.01


Consensus pattern (41 bp):   
GGCGGCGGAAGAAGGAAGGAGGAGGCGGGGAGAAGAAGGAA

Found at i:724 original size:18 final size:19

Alignment explanation


    Indices: 670--794  Score: 105
    Period size: 21  Copynumber: 6.3  Consensus size: 19

        660 TGCTGCAGGC

                                  
        670 GGCGGCGG-GAAGAAGGGAGGA
          1 GGCGGCGGAGAAGAA-GGA--A

              *  *             
        691 GGAGGTGGAG-AGAAGGAA
          1 GGCGGCGGAGAAGAAGGAA

                                    
        709 GGCGGCGAGAAGAAGGAAGGAGGA
          1 GGCGGCG-G-AGAA-GAAGGA--A

                               
        733 GGCGG-GGAGAAGAAGGAA
          1 GGCGGCGGAGAAGAAGGAA

                                 
        751 GGCGGCGGAGAGAAGAAGGAA
          1 GGCGGC-G-GAGAAGAAGGAA

                           *   
        772 GGCGG-GGAGAAGAAAGAA
          1 GGCGGCGGAGAAGAAGGAA

                 
        790 GGCGG
          1 GGCGG

        795 TGGTGAAGCC


Statistics
Matches: 89,  Mismatches: 5, Indels: 23
        0.76            0.04        0.20

Matches are distributed among these distances:
  18   28  0.31
  19    2  0.02
  20   12  0.13
  21   32  0.36
  22    8  0.09
  23    1  0.01
  24    6  0.07

ACGTcount: A:0.36, C:0.07, G:0.56, T:0.01


Consensus pattern (19 bp):   
GGCGGCGGAGAAGAAGGAA

Done.