Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_00339

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, 835

Length: 1392
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26


Found at i:664 original size:21 final size:21

Alignment explanation


    Indices: 638--677  Score: 80
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        628 ATAGCTCCAC

                                 
        638 CAAGGTTTTCATTTGATGATT
          1 CAAGGTTTTCATTTGATGATT

                               
        659 CAAGGTTTTCATTTGATGA
          1 CAAGGTTTTCATTTGATGA

        678 ACCAAGAGCT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45


Consensus pattern (21 bp):   
CAAGGTTTTCATTTGATGATT

Found at i:683 original size:21 final size:21

Alignment explanation


    Indices: 636--683  Score: 78
    Period size: 21  Copynumber: 2.3  Consensus size: 21

        626 ATATAGCTCC

                                 
        636 ACCAAGGTTTTCATTTGATGA
          1 ACCAAGGTTTTCATTTGATGA

            **                   
        657 TTCAAGGTTTTCATTTGATGA
          1 ACCAAGGTTTTCATTTGATGA

                  
        678 ACCAAG
          1 ACCAAG

        684 AGCTTCTTGG


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38


Consensus pattern (21 bp):   
ACCAAGGTTTTCATTTGATGA
Done.