Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_38265

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, 907

Length: 1512
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27


Found at i:1038 original size:18 final size:17

Alignment explanation


    Indices: 1017--1076  Score: 52
    Period size: 18  Copynumber: 3.4  Consensus size: 17

       1007 TTGACAACCA

                              
       1017 TGATGATGAGCTTGTATC
          1 TGATGATGA-CTTGTATC

                       *       
       1035 TGATGA--ACTGGATGATC
          1 TGATGATGACTTG-T-ATC

                               
       1052 TGGATGATGAACTTGTATC
          1 T-GATGATG-ACTTGTATC

                  
       1071 TGATGA
          1 TGATGA

       1077 ATTTGATGAC


Statistics
Matches: 34,  Mismatches: 2, Indels: 12
        0.71            0.04        0.25

Matches are distributed among these distances:
  15    3  0.09
  16    2  0.06
  17    4  0.12
  18   16  0.47
  19    4  0.12
  20    1  0.03
  21    4  0.12

ACGTcount: A:0.27, C:0.10, G:0.28, T:0.35


Consensus pattern (17 bp):   
TGATGATGACTTGTATC

Found at i:1040 original size:36 final size:36

Alignment explanation


    Indices: 993--1098  Score: 124
    Period size: 36  Copynumber: 2.9  Consensus size: 36

        983 CATTGGAAAG

                         *    **                
        993 TGTATCTGATGAAGTTGACAACCATGATGATGAGCT
          1 TGTATCTGATGAACTTGATGACCATGATGATGAGCT

                           *     *            *  
       1029 TGTATCTGATGAACTGGATGATC-TGGATGATGAACT
          1 TGTATCTGATGAACTTGATGACCAT-GATGATGAGCT

                         *          *         
       1065 TGTATCTGATGAATTTGATGACCAAGATGATGAG
          1 TGTATCTGATGAACTTGATGACCATGATGATGAG

       1099 TTTGATGAAG


Statistics
Matches: 57,  Mismatches: 11, Indels: 4
        0.79            0.15        0.06

Matches are distributed among these distances:
  35    1  0.02
  36   56  0.98

ACGTcount: A:0.30, C:0.11, G:0.26, T:0.32


Consensus pattern (36 bp):   
TGTATCTGATGAACTTGATGACCATGATGATGAGCT
Done.