Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_27768

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, 745

Length: 1242
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28


Found at i:650 original size:27 final size:27

Alignment explanation


    Indices: 620--713  Score: 116
    Period size: 27  Copynumber: 3.4  Consensus size: 27

        610 AACGATCACC

                       *      *        
        620 ACCACCACCACGACGAACTCTTGCATG
          1 ACCACCACCACCACGAACACTTGCATG

                         *             
        647 ACCACCACCACCATGAACACTTGCATG
          1 ACCACCACCACCACGAACACTTGCATG

                                   *      
        674 ACCACCACCACCACCACGAACACCTGCATG
          1 ---ACCACCACCACCACGAACACTTGCATG

                *     
        704 ACCAACACCA
          1 ACCACCACCA

        714 TGAACATCAT


Statistics
Matches: 58,  Mismatches: 6, Indels: 6
        0.83            0.09        0.09

Matches are distributed among these distances:
  27   33  0.57
  30   25  0.43

ACGTcount: A:0.34, C:0.45, G:0.11, T:0.11


Consensus pattern (27 bp):   
ACCACCACCACCACGAACACTTGCATG

Found at i:651 original size:30 final size:29

Alignment explanation


    Indices: 617--713  Score: 126
    Period size: 30  Copynumber: 3.3  Consensus size: 29

        607 GGGAACGATC

                                 *        
        617 ACCACCACCACCACGACGAACTCTTGCATG
          1 ACCACCACCACCAC-ACGAACACTTGCATG

                           *             
        647 ACCACCACCA-C-CATGAACACTTGCATG
          1 ACCACCACCACCACACGAACACTTGCATG

                                   *      
        674 ACCACCACCACCACCACGAACACCTGCATG
          1 ACCACCACCACCA-CACGAACACTTGCATG

                *     
        704 ACCAACACCA
          1 ACCACCACCA

        714 TGAACATCAT


Statistics
Matches: 59,  Mismatches: 5, Indels: 6
        0.84            0.07        0.09

Matches are distributed among these distances:
  27   23  0.39
  28    2  0.03
  29    1  0.02
  30   33  0.56

ACGTcount: A:0.34, C:0.45, G:0.10, T:0.10


Consensus pattern (29 bp):   
ACCACCACCACCACACGAACACTTGCATG

Found at i:731 original size:57 final size:56

Alignment explanation


    Indices: 617--724  Score: 148
    Period size: 57  Copynumber: 1.9  Consensus size: 56

        607 GGGAACGATC

                          *      * *                          *      
        617 ACCACCACCACCACGACGAACTCTTGCATGACCACCACCACCATGAACACTTGCATG
          1 ACCACCACCACCACCACGAACACCTGCATGACCA-CACCACCATGAACACATGCATG

                                                                 
        674 ACCACCACCACCACCACGAACACCTGCATGACCA-A-CACCATGAACATCATG
          1 ACCACCACCACCACCACGAACACCTGCATGACCACACCACCATGAACA-CATG

        725 ACCATGAGGC


Statistics
Matches: 46,  Mismatches: 4, Indels: 4
        0.85            0.07        0.07

Matches are distributed among these distances:
  54   11  0.24
  55    4  0.09
  57   31  0.67

ACGTcount: A:0.34, C:0.43, G:0.11, T:0.12


Consensus pattern (56 bp):   
ACCACCACCACCACCACGAACACCTGCATGACCACACCACCATGAACACATGCATG
Done.