Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_06443

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: 2913
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20


Found at i:1487 original size:24 final size:24

Alignment explanation


    Indices: 1450--1501  Score: 77
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       1440 TTCCCCGGTA

                              *     
       1450 GAAGTCAAAACCGAAAAAGGGTCT
          1 GAAGTCAAAACCGAAAAAAGGTCT

                  *  *              
       1474 GAAGTCGAATCCGAAAAAAGGTCT
          1 GAAGTCAAAACCGAAAAAAGGTCT

                
       1498 GAAG
          1 GAAG

       1502 AACACGTCCA


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.44, C:0.15, G:0.27, T:0.13


Consensus pattern (24 bp):   
GAAGTCAAAACCGAAAAAAGGTCT

Found at i:1611 original size:48 final size:48

Alignment explanation


    Indices: 1544--1727  Score: 271
    Period size: 48  Copynumber: 3.8  Consensus size: 48

       1534 GCCATGGCCG

                 *        *             *       *          *
       1544 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGTAGAGAAAGCCG
          1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGAAAGCCA

                                                             
       1592 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGA-AGAAGCCA
          1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGA-AAGCCA

                 *                                *  *      
       1640 ATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAAAGGAAGCCA
          1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGAAAGCCA

                   *                                
       1688 ATGAACCAAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGA
          1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGA

       1728 AGAAGGAAGC


Statistics
Matches: 123,  Mismatches: 11, Indels: 4
        0.89            0.08        0.03

Matches are distributed among these distances:
  47    1  0.01
  48  122  0.99

ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21


Consensus pattern (48 bp):   
ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGAAAGCCA

Found at i:1708 original size:96 final size:96

Alignment explanation


    Indices: 1544--1732  Score: 315
    Period size: 96  Copynumber: 2.0  Consensus size: 96

       1534 GCCATGGCCG

                                                * *        *       *         
       1544 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGTAGAGAAAGCCGATGAACCGAAAGCAGTA
          1 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGCAAAGAAAGCCAATGAACCAAAAGCAGTA

                                           
       1609 AGTTCTGTTCCGAAATCTGCAGAAGAAGCCA
         66 AGTTCTGTTCCGAAATCTGCAGAAGAAGCCA

                          *             *            *                       
       1640 ATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAAAGGAAGCCAATGAACCAAAAGCAGTA
          1 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGCAAAGAAAGCCAATGAACCAAAAGCAGTA

                                        
       1705 AGTTCTGTTCCGAAATCTGCAGAAGAAG
         66 AGTTCTGTTCCGAAATCTGCAGAAGAAG

       1733 GAAGCGTTAG


Statistics
Matches: 86,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  96   86  1.00

ACGTcount: A:0.39, C:0.19, G:0.22, T:0.21


Consensus pattern (96 bp):   
ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGCAAAGAAAGCCAATGAACCAAAAGCAGTA
AGTTCTGTTCCGAAATCTGCAGAAGAAGCCA

Found at i:2136 original size:9 final size:9

Alignment explanation


    Indices: 2124--2182  Score: 57
    Period size: 9  Copynumber: 6.6  Consensus size: 9

       2114 CAATTCCAGC

                     
       2124 AGAAGAGAA
          1 AGAAGAGAA

                 *   
       2133 AGAAGTGAA
          1 AGAAGAGAA

            *         
       2142 GGAAGTA-AA
          1 AGAAG-AGAA

                 *   
       2151 AGAAGTGAA
          1 AGAAGAGAA

             *       
       2160 ACAAGAGAA
          1 AGAAGAGAA

                *    
       2169 AGAAAAGAA
          1 AGAAGAGAA

                 
       2178 AGAAG
          1 AGAAG

       2183 TAGCTCTGGG


Statistics
Matches: 38,  Mismatches: 10, Indels: 4
        0.73            0.19        0.08

Matches are distributed among these distances:
   9   38  1.00

ACGTcount: A:0.63, C:0.02, G:0.31, T:0.05


Consensus pattern (9 bp):   
AGAAGAGAA

Done.