Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_35780

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, 402

Length: 671
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.24


Found at i:335 original size:72 final size:72

Alignment explanation


    Indices: 242--382  Score: 228
    Period size: 72  Copynumber: 2.0  Consensus size: 72

        232 AGTCCGAGCG

                                                                   *         
        242 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACTATTTCCCGG
          1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG

                   
        307 GCTCGTC
         66 GCTCGTC

                       *    *                         *  *               *   
        314 ATCGCATTCACTTTCGGCTGATACTTCTTATCATCCGGATTTTGCGGGCAATGACAATTTCTCGG
          1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG

                
        379 GCTC
         66 GCTC

        383 ATCGGGGGGC


Statistics
Matches: 63,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  72   63  1.00

ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33


Consensus pattern (72 bp):   
ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG
GCTCGTC

Found at i:476 original size:33 final size:33

Alignment explanation


    Indices: 430--503  Score: 87
    Period size: 33  Copynumber: 2.2  Consensus size: 33

        420 GGGTCGTACA

                                *             
        430 CACCGCAGCATAGCACCT-CTCCCGGCCCATATC
          1 CACCGCAGCATAGCA-CTGCCCCCGGCCCATATC

                   **                   *    
        463 CACCGCATTATAGCACTGCCCCCGGCCCGTATC
          1 CACCGCAGCATAGCACTGCCCCCGGCCCATATC

               *    
        496 CACTGCAG
          1 CACCGCAG

        504 TACTCCACTC


Statistics
Matches: 34,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  32    2  0.06
  33   32  0.94

ACGTcount: A:0.20, C:0.46, G:0.18, T:0.16


Consensus pattern (33 bp):   
CACCGCAGCATAGCACTGCCCCCGGCCCATATC
Done.