Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_09031

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: 2121
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27


Found at i:2056 original size:9 final size:9

Alignment explanation


    Indices: 2044--2075  Score: 55
    Period size: 9  Copynumber: 3.6  Consensus size: 9

       2034 TGCATCAGCT

                     
       2044 GCAGCCGCA
          1 GCAGCCGCA

                    *
       2053 GCAGCCGCT
          1 GCAGCCGCA

                     
       2062 GCAGCCGCA
          1 GCAGCCGCA

                 
       2071 GCAGC
          1 GCAGC

       2076 AACTGCTGCA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   9   21  1.00

ACGTcount: A:0.19, C:0.44, G:0.34, T:0.03


Consensus pattern (9 bp):   
GCAGCCGCA

Found at i:2064 original size:18 final size:18

Alignment explanation


    Indices: 2041--2075  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2031 AGCTGCATCA

                              
       2041 GCTGCAGCCGCAGCAGCC
          1 GCTGCAGCCGCAGCAGCC

                             
       2059 GCTGCAGCCGCAGCAGC
          1 GCTGCAGCCGCAGCAGC

       2076 AACTGCTGCA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.17, C:0.43, G:0.34, T:0.06


Consensus pattern (18 bp):   
GCTGCAGCCGCAGCAGCC

Found at i:2081 original size:18 final size:18

Alignment explanation


    Indices: 2042--2081  Score: 62
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       2032 GCTGCATCAG

                            **
       2042 CTGCAGCCGCAGCAGCCG
          1 CTGCAGCCGCAGCAGCAA

                              
       2060 CTGCAGCCGCAGCAGCAA
          1 CTGCAGCCGCAGCAGCAA

                
       2078 CTGC
          1 CTGC

       2082 TGCAGCTAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.20, C:0.42, G:0.30, T:0.07


Consensus pattern (18 bp):   
CTGCAGCCGCAGCAGCAA
Done.