Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_29946

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: 5727
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27


Found at i:4274 original size:30 final size:30

Alignment explanation


    Indices: 4240--4307  Score: 73
    Period size: 33  Copynumber: 2.2  Consensus size: 30

       4230 TGTTTATGAG

                                          
       4240 GAAACAACCATTCCTGCAACCTTAGGTCAA
          1 GAAACAACCATTCCTGCAACCTTAGGTCAA

                    *   *             *   *  
       4270 GAAACTCCCACCTTTCCTGCAACCTTGGGTGAA
          1 GAAA---CAACCATTCCTGCAACCTTAGGTCAA

                 
       4303 GAAAC
          1 GAAAC

       4308 TTGTAGCACT


Statistics
Matches: 31,  Mismatches: 4, Indels: 6
        0.76            0.10        0.15

Matches are distributed among these distances:
  30    5  0.16
  33   26  0.84

ACGTcount: A:0.32, C:0.31, G:0.16, T:0.21


Consensus pattern (30 bp):   
GAAACAACCATTCCTGCAACCTTAGGTCAA

Found at i:4529 original size:33 final size:33

Alignment explanation


    Indices: 4457--4529  Score: 76
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       4447 GTTCCTCTGA

                   **           * *    *     
       4457 CTTTCAGTGAAGAAACTCCTGCCATTCTTCCAT
          1 CTTTCAGCAAAGAAACTCCTACAATTCCTCCAT

             *                               
       4490 CATTCAGCAAAGAAACTCCTACAATTCCT-CAT
          1 CTTTCAGCAAAGAAACTCCTACAATTCCTCCAT

                    
       4522 CCTTTCAG
          1 -CTTTCAG

       4530 TGAGGGAACT


Statistics
Matches: 32,  Mismatches: 7, Indels: 2
        0.78            0.17        0.05

Matches are distributed among these distances:
  32    3  0.09
  33   29  0.91

ACGTcount: A:0.29, C:0.32, G:0.10, T:0.30


Consensus pattern (33 bp):   
CTTTCAGCAAAGAAACTCCTACAATTCCTCCAT

Found at i:4604 original size:33 final size:33

Alignment explanation


    Indices: 4567--4637  Score: 90
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       4557 ATCGGGTCCA

                            *      *          
       4567 GAAACT-CAGACCATTTCTACAACCATGGGTGAG
          1 GAAACTACA-ACCATTCCTACAAACATGGGTGAG

                              *     *        
       4600 GAAACTACAACCATTCCTGCAAACTTGGGTGAG
          1 GAAACTACAACCATTCCTACAAACATGGGTGAG

                 
       4633 GAAAC
          1 GAAAC

       4638 AACTGCTACT


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  33   31  0.94
  34    2  0.06

ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20


Consensus pattern (33 bp):   
GAAACTACAACCATTCCTACAAACATGGGTGAG
Done.