Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_08942

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: 7299
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26


Found at i:210 original size:15 final size:15

Alignment explanation


    Indices: 145--217  Score: 68
    Period size: 15  Copynumber: 5.3  Consensus size: 15

        135 AGACAACGCC

                       *   
        145 CAGCAGCAACAGCAG
          1 CAGCAGCAACAACAG

                   *       
        160 CAGCAGCCAC-A-AG
          1 CAGCAGCAACAACAG

                           
        173 -AGCAGCAACAACA-
          1 CAGCAGCAACAACAG

                           
        186 -AG-AGCAACAACAG
          1 CAGCAGCAACAACAG

                   *     * 
        199 CAGCAGCCACAACCG
          1 CAGCAGCAACAACAG

                
        214 CAGC
          1 CAGC

        218 TGCCGCGAAA


Statistics
Matches: 48,  Mismatches: 5, Indels: 10
        0.76            0.08        0.16

Matches are distributed among these distances:
  12   18  0.38
  13    5  0.10
  14    3  0.06
  15   22  0.46

ACGTcount: A:0.42, C:0.36, G:0.22, T:0.00


Consensus pattern (15 bp):   
CAGCAGCAACAACAG

Found at i:280 original size:18 final size:18

Alignment explanation


    Indices: 246--284  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

        236 AACTGGTCAA

                       *      
        246 GGTTAAGAAAGTAGTGGT
          1 GGTTAAGAAAGAAGTGGT

                               
        264 GGTTAAG-AAGAAGGTGGT
          1 GGTTAAGAAAGAA-GTGGT

               
        282 GGT
          1 GGT

        285 GGGAGCAGCA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  17    4  0.21
  18   15  0.79

ACGTcount: A:0.31, C:0.00, G:0.44, T:0.26


Consensus pattern (18 bp):   
GGTTAAGAAAGAAGTGGT
Done.