Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_07472

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, 1000

Length: 1821
ACGTcount: A:0.41, C:0.15, G:0.27, T:0.18


Found at i:1101 original size:3 final size:3

Alignment explanation


    Indices: 1093--1163  Score: 58
    Period size: 3  Copynumber: 23.7  Consensus size: 3

       1083 GGATGAGTCT

                              *   *                                     
       1093 GAA GAA GAA GAA GAG GAG GAA GAA GAA GAA -AA GGAA GAA GAA G-A
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA

                       *      *                 
       1137 GAA GGAA GAG GAA -CA GAA TGAA GAA GA
          1 GAA -GAA GAA GAA GAA GAA -GAA GAA GA

       1164 GAAAAATGAA


Statistics
Matches: 56,  Mismatches: 6, Indels: 12
        0.76            0.08        0.16

Matches are distributed among these distances:
   2    5  0.09
   3   43  0.77
   4    8  0.14

ACGTcount: A:0.59, C:0.01, G:0.38, T:0.01


Consensus pattern (3 bp):   
GAA

Found at i:1116 original size:15 final size:15

Alignment explanation


    Indices: 1096--1163  Score: 91
    Period size: 15  Copynumber: 4.5  Consensus size: 15

       1086 TGAGTCTGAA

                        *  
       1096 GAAGAAGAAGAGGAG
          1 GAAGAAGAAGAGAAG

                       *   
       1111 GAAGAAGAAGAAAAG
          1 GAAGAAGAAGAGAAG

                           
       1126 GAAGAAGAAGAGAAG
          1 GAAGAAGAAGAGAAG

                 *   *    *
       1141 GAAGAGGAACAGAAT
          1 GAAGAAGAAGAGAAG

                    
       1156 GAAGAAGA
          1 GAAGAAGA

       1164 GAAAAATGAA


Statistics
Matches: 46,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  15   46  1.00

ACGTcount: A:0.59, C:0.01, G:0.38, T:0.01


Consensus pattern (15 bp):   
GAAGAAGAAGAGAAG

Found at i:1144 original size:27 final size:25

Alignment explanation


    Indices: 1097--1166  Score: 77
    Period size: 27  Copynumber: 2.6  Consensus size: 25

       1087 GAGTCTGAAG

                      *               
       1097 AAGAAGAAGAGGAGGAAGAAGAAGAA
          1 AAGAAGAAGAAGA-GAAGAAGAAGAA

                                   *   
       1123 AAGGAAGAAGAAGAGAAGGAAGAGGAA
          1 AA-GAAGAAGAAGAGAA-GAAGAAGAA

            *                
       1150 CAGAATGAAGAAGAGAA
          1 AAGAA-GAAGAAGAGAA

       1167 AAATGAAAAT


Statistics
Matches: 38,  Mismatches: 3, Indels: 5
        0.83            0.07        0.11

Matches are distributed among these distances:
  26    8  0.21
  27   30  0.79

ACGTcount: A:0.60, C:0.01, G:0.37, T:0.01


Consensus pattern (25 bp):   
AAGAAGAAGAAGAGAAGAAGAAGAA
Done.