Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_03333

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: 2901
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27


Found at i:2020 original size:21 final size:21

Alignment explanation


    Indices: 1988--2046  Score: 64
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       1978 ACTGAACTGC

                              *   
       1988 AGAAGAAAATCCTGGAGCGCGT
          1 AGAAG-AAATCCTGGAGCACGT

            *            *    *  
       2010 TGAAGAAATCCTGAAGCATGT
          1 AGAAGAAATCCTGGAGCACGT

             *              
       2031 ACAAGAAATCCTGGAG
          1 AGAAGAAATCCTGGAG

       2047 TGTGTTAAGG


Statistics
Matches: 30,  Mismatches: 7, Indels: 1
        0.79            0.18        0.03

Matches are distributed among these distances:
  21   26  0.87
  22    4  0.13

ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17


Consensus pattern (21 bp):   
AGAAGAAATCCTGGAGCACGT

Found at i:2168 original size:12 final size:12

Alignment explanation


    Indices: 2153--2177  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       2143 CACCCCTCAT

                        
       2153 TGTTGAAGCAGC
          1 TGTTGAAGCAGC

                        
       2165 TGTTGAAGCAGC
          1 TGTTGAAGCAGC

             
       2177 T
          1 T

       2178 TCCAGACCTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28


Consensus pattern (12 bp):   
TGTTGAAGCAGC
Done.