Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_27042

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: 2613
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23


Found at i:102 original size:21 final size:21

Alignment explanation


    Indices: 76--155  Score: 90
    Period size: 21  Copynumber: 3.8  Consensus size: 21

         66 AAATGTAGAA

                    *   *        
         76 GCAGTGAAGCAAGGTGAAAAG
          1 GCAGTGAACCAAAGTGAAAAG

                                 
         97 GCAGTGAACCAAAGTGAAAAG
          1 GCAGTGAACCAAAGTGAAAAG

              *          *       
        118 GCTGTGAACCAAAATG-AAAG
          1 GCAGTGAACCAAAGTGAAAAG

             **               
        138 AATAGTGAACCAAAGTGA
          1 -GCAGTGAACCAAAGTGA

        156 GGAAGCGTTT


Statistics
Matches: 49,  Mismatches: 8, Indels: 3
        0.82            0.13        0.05

Matches are distributed among these distances:
  20    4  0.08
  21   45  0.92

ACGTcount: A:0.46, C:0.12, G:0.29, T:0.12


Consensus pattern (21 bp):   
GCAGTGAACCAAAGTGAAAAG

Found at i:1256 original size:24 final size:24

Alignment explanation


    Indices: 1213--1258  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       1203 CATAGCCCCA

                        * *         
       1213 AAACACAAAAAGCAGGCATCTAAG
          1 AAACACAAAAAGAACGCATCTAAG

                           *      
       1237 AAACACAAAAAGAACTCATCTA
          1 AAACACAAAAAGAACGCATCTA

       1259 CAGGTCCTGC


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.57, C:0.22, G:0.11, T:0.11


Consensus pattern (24 bp):   
AAACACAAAAAGAACGCATCTAAG
Done.