Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_13876

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, 867

Length: 1446
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25


Found at i:160 original size:15 final size:15

Alignment explanation


    Indices: 135--172  Score: 51
    Period size: 15  Copynumber: 2.5  Consensus size: 15

        125 AGACCATGGA

                  *        
        135 AGAAGAGGTGGA-GT
          1 AGAAGAAGTGGAGGT

                            
        149 ATGAAGAAGTGGAGGT
          1 A-GAAGAAGTGGAGGT

                    
        165 AGAAGAAG
          1 AGAAGAAG

        173 AAGGAGAGGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  14    1  0.05
  15   17  0.81
  16    3  0.14

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


Consensus pattern (15 bp):   
AGAAGAAGTGGAGGT

Found at i:171 original size:3 final size:3

Alignment explanation


    Indices: 165--233  Score: 77
    Period size: 3  Copynumber: 23.0  Consensus size: 3

        155 AAGTGGAGGT

                          *     *                    *     * *          
        165 AGA AGA AGA AGG AGA GGA AGA A-A TAGA AGA GGA AGT GGA AGA AGA
          1 AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA

                                           
        210 AGA AGA AGA AGA AGA AGA AGA AGA
          1 AGA AGA AGA AGA AGA AGA AGA AGA

        234 CCTGGATGTT


Statistics
Matches: 54,  Mismatches: 10, Indels: 4
        0.79            0.15        0.06

Matches are distributed among these distances:
   2    1  0.02
   3   52  0.96
   4    1  0.02

ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03


Consensus pattern (3 bp):   
AGA

Found at i:172 original size:18 final size:17

Alignment explanation


    Indices: 151--211  Score: 52
    Period size: 18  Copynumber: 3.4  Consensus size: 17

        141 GGTGGAGTAT

                              
        151 GAAGAAGTGGAGGTAGAA
          1 GAAGAAG-GGAGGTAGAA

                         *    
        169 GAAGAAGGAGAGGAAGAA
          1 GAAGAAGG-GAGGTAGAA

                        *  *   
        187 -ATAGAAGAGGAAGTGGAA
          1 GA-AGAAG-GGAGGTAGAA

                   
        205 GAAGAAG
          1 GAAGAAG

        212 AAGAAGAAGA


Statistics
Matches: 35,  Mismatches: 4, Indels: 8
        0.74            0.09        0.17

Matches are distributed among these distances:
  17    2  0.06
  18   31  0.89
  19    2  0.06

ACGTcount: A:0.51, C:0.00, G:0.43, T:0.07


Consensus pattern (17 bp):   
GAAGAAGGGAGGTAGAA

Done.