Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_35259

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: 3176
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26


Found at i:2269 original size:33 final size:33

Alignment explanation


    Indices: 2178--2294  Score: 92
    Period size: 33  Copynumber: 3.5  Consensus size: 33

       2168 AATCCGGACT

                  * *          *    *    *   
       2178 AGTAGCTGGGATGATGCCCTTATATGCAGCCCA
          1 AGTAGCAGCGATGATGCCCCTATAAGCAGGCCA

                 *           ** **            
       2211 AGTAGTAG-GAATGATGTTCAAATAAGCAGGCCA
          1 AGTAGCAGCG-ATGATGCCCCTATAAGCAGGCCA

                    *    *                ** 
       2244 AGTAGCAGTGATGGTGCCCCTATAAGCAGGTTA
          1 AGTAGCAGCGATGATGCCCCTATAAGCAGGCCA

                              
       2277 AGTAGCAGCGATGATGCC
          1 AGTAGCAGCGATGATGCC

       2295 TCAATAATCA


Statistics
Matches: 64,  Mismatches: 18, Indels: 4
        0.74            0.21        0.05

Matches are distributed among these distances:
  32    1  0.02
  33   62  0.97
  34    1  0.02

ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22


Consensus pattern (33 bp):   
AGTAGCAGCGATGATGCCCCTATAAGCAGGCCA

Found at i:2307 original size:33 final size:33

Alignment explanation


    Indices: 2231--2313  Score: 103
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       2221 ATGATGTTCA

                      **         *    *      
       2231 AATAAGCAGGCCAAGTAGCAGTGATGGTGCCCC
          1 AATAAGCAGGTTAAGTAGCAGCGATGATGCCCC

            *                              * 
       2264 TATAAGCAGGTTAAGTAGCAGCGATGATGCCTC
          1 AATAAGCAGGTTAAGTAGCAGCGATGATGCCCC

                 *           
       2297 AATAATCAGGTTAAGTA
          1 AATAAGCAGGTTAAGTA

       2314 TTGGGGGAAA


Statistics
Matches: 42,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  33   42  1.00

ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22


Consensus pattern (33 bp):   
AATAAGCAGGTTAAGTAGCAGCGATGATGCCCC
Done.