Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_08266

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, 831

Length: 1386
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26


Found at i:1061 original size:6 final size:6

Alignment explanation


    Indices: 1050--1079  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       1040 ACTGTAGTGC

                                              
       1050 AGATGA AGATGA AGATGA AGATGA AGATGA
          1 AGATGA AGATGA AGATGA AGATGA AGATGA

       1080 TGAAATCGAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17


Consensus pattern (6 bp):   
AGATGA

Found at i:1083 original size:21 final size:21

Alignment explanation


    Indices: 1050--1096  Score: 55
    Period size: 18  Copynumber: 2.4  Consensus size: 21

       1040 ACTGTAGTGC

                           *     
       1050 AGATGAAGATGA--AGAT-GA
          1 AGATGAAGATGATGAAATCGA

                                 
       1068 AGATGAAGATGATGAAATCGA
          1 AGATGAAGATGATGAAATCGA

              *     
       1089 AGCTGAAG
          1 AGATGAAG

       1097 TCGAGTCATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  18   12  0.50
  20    3  0.12
  21    9  0.38

ACGTcount: A:0.47, C:0.04, G:0.32, T:0.17


Consensus pattern (21 bp):   
AGATGAAGATGATGAAATCGA
Done.