Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_01122

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, 828

Length: 1380
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19


Found at i:1163 original size:12 final size:12

Alignment explanation


    Indices: 1143--1194  Score: 50
    Period size: 12  Copynumber: 4.3  Consensus size: 12

       1133 ATGAAGAGCA

                *       
       1143 AAAGACAGAGAC
          1 AAAGGCAGAGAC

             *         *
       1155 AGAGGCAGAGAA
          1 AAAGGCAGAGAC

                *     * 
       1167 AAAGACAGAGCC
          1 AAAGGCAGAGAC

                      * 
       1179 AAAGGCAGAGGC
          1 AAAGGCAGAGAC

                
       1191 AAAG
          1 AAAG

       1195 CAAAAGGCGG


Statistics
Matches: 31,  Mismatches: 9, Indels: 0
        0.77            0.22        0.00

Matches are distributed among these distances:
  12   31  1.00

ACGTcount: A:0.52, C:0.15, G:0.33, T:0.00


Consensus pattern (12 bp):   
AAAGGCAGAGAC

Found at i:1164 original size:24 final size:24

Alignment explanation


    Indices: 1137--1193  Score: 78
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       1127 ATGCTGATGA

                               *    
       1137 AGAGCAAAAGACAGAGACAGAGGC
          1 AGAGCAAAAGACAGAGACAAAGGC

                *           *       
       1161 AGAGAAAAAGACAGAGCCAAAGGC
          1 AGAGCAAAAGACAGAGACAAAGGC

                     
       1185 AGAGGCAAA
          1 AGA-GCAAA

       1194 GCAAAAGGCG


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  24   24  0.86
  25    4  0.14

ACGTcount: A:0.53, C:0.16, G:0.32, T:0.00


Consensus pattern (24 bp):   
AGAGCAAAAGACAGAGACAAAGGC

Done.