Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_14707

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: 3021
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25


Found at i:1610 original size:6 final size:6

Alignment explanation


    Indices: 1599--1669  Score: 133
    Period size: 6  Copynumber: 11.8  Consensus size: 6

       1589 TTGGAGAATC

                                                                   
       1599 GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA
          1 GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA

                                 *    
       1647 GGAAGA GGAAGA GGAAGA AGAAG
          1 GGAAGA GGAAGA GGAAGA GGAAG

       1670 CAGAAGCAGA


Statistics
Matches: 64,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
   6   64  1.00

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


Consensus pattern (6 bp):   
GGAAGA

Found at i:1674 original size:6 final size:6

Alignment explanation


    Indices: 1660--1705  Score: 74
    Period size: 6  Copynumber: 7.7  Consensus size: 6

       1650 AGAGGAAGAG

                *                                         *      
       1660 GAAGAA GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA GAAGAA GAAG
          1 GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA GAAG

       1706 AGGAAGAAGA


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   6   38  1.00

ACGTcount: A:0.54, C:0.11, G:0.35, T:0.00


Consensus pattern (6 bp):   
GAAGCA

Found at i:1675 original size:12 final size:12

Alignment explanation


    Indices: 1660--1716  Score: 80
    Period size: 12  Copynumber: 4.8  Consensus size: 12

       1650 AGAGGAAGAG

                        
       1660 GAAGAAGAAGCA
          1 GAAGAAGAAGCA

                *       
       1672 GAAGCAGAAGCA
          1 GAAGAAGAAGCA

                *       
       1684 GAAGCAGAAGCA
          1 GAAGAAGAAGCA

                        
       1696 GAAGAAGAAG-A
          1 GAAGAAGAAGCA

                      
       1707 GGAAGAAGAA
          1 -GAAGAAGAA

       1717 AAACTTAAGC


Statistics
Matches: 42,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  11    1  0.02
  12   41  0.98

ACGTcount: A:0.56, C:0.09, G:0.35, T:0.00


Consensus pattern (12 bp):   
GAAGAAGAAGCA

Found at i:1716 original size:18 final size:18

Alignment explanation


    Indices: 1599--1712  Score: 128
    Period size: 18  Copynumber: 6.3  Consensus size: 18

       1589 TTGGAGAATC

                        *     
       1599 GGAAGAGGAAGAGGAAGA
          1 GGAAGAGGAAGAAGAAGA

                        *     
       1617 GGAAGAGGAAGAGGAAGA
          1 GGAAGAGGAAGAAGAAGA

                        *     
       1635 GGAAGAGGAAGAGGAAGA
          1 GGAAGAGGAAGAAGAAGA

                               
       1653 GGAAGAGGAAGAAGAAGCA
          1 GGAAGAGGAAGAAGAAG-A

                        *       
       1672 -GAAGCA-GAAGCAGAAGCA
          1 GGAAG-AGGAAGAAGAAG-A

                               
       1690 -GAAGCA-GAAGAAGAAGA
          1 GGAAG-AGGAAGAAGAAGA

                  
       1707 GGAAGA
          1 GGAAGA

       1713 AGAAAAACTT


Statistics
Matches: 90,  Mismatches: 3, Indels: 7
        0.90            0.03        0.07

Matches are distributed among these distances:
  17    2  0.02
  18   86  0.96
  19    2  0.02

ACGTcount: A:0.52, C:0.04, G:0.44, T:0.00


Consensus pattern (18 bp):   
GGAAGAGGAAGAAGAAGA
Done.