Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_27319

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: 2501
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29


Found at i:1899 original size:6 final size:6

Alignment explanation


    Indices: 1888--1921  Score: 68
    Period size: 6  Copynumber: 5.7  Consensus size: 6

       1878 TCTGTCATTA

                                                   
       1888 ATGACC ATGACC ATGACC ATGACC ATGACC ATGA
          1 ATGACC ATGACC ATGACC ATGACC ATGACC ATGA

       1922 AAATGACACA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   28  1.00

ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18


Consensus pattern (6 bp):   
ATGACC

Found at i:1927 original size:12 final size:12

Alignment explanation


    Indices: 1887--1928  Score: 57
    Period size: 12  Copynumber: 3.5  Consensus size: 12

       1877 TTCTGTCATT

                        
       1887 AATGACCATGAC
          1 AATGACCATGAC

            *           
       1899 CATGACCATGAC
          1 AATGACCATGAC

            *          *
       1911 CATGACCATGAA
          1 AATGACCATGAC

                  
       1923 AATGAC
          1 AATGAC

       1929 ACAGAAAAAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  12   27  1.00

ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17


Consensus pattern (12 bp):   
AATGACCATGAC

Found at i:1927 original size:18 final size:18

Alignment explanation


    Indices: 1887--1928  Score: 66
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       1877 TTCTGTCATT

                             *
       1887 AATGACCATGACCATGAC
          1 AATGACCATGACCATGAA

            *                 
       1905 CATGACCATGACCATGAA
          1 AATGACCATGACCATGAA

                  
       1923 AATGAC
          1 AATGAC

       1929 ACAGAAAAAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17


Consensus pattern (18 bp):   
AATGACCATGACCATGAA
Done.