Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_18035

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, 516

Length: 861
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28


Found at i:598 original size:3 final size:3

Alignment explanation


    Indices: 590--628  Score: 51
    Period size: 3  Copynumber: 13.0  Consensus size: 3

        580 ATGATCACGA

                                 *   *                   *     
        590 CAT CAT CAT CAT CAT CTT CTT CAT CAT CAT CAT CTT CAT
          1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT

        629 ACTGGGTTTC


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41


Consensus pattern (3 bp):   
CAT

Found at i:615 original size:15 final size:15

Alignment explanation


    Indices: 590--628  Score: 60
    Period size: 15  Copynumber: 2.6  Consensus size: 15

        580 ATGATCACGA

                *          
        590 CATCATCATCATCAT
          1 CATCTTCATCATCAT

             *             
        605 CTTCTTCATCATCAT
          1 CATCTTCATCATCAT

                     
        620 CATCTTCAT
          1 CATCTTCAT

        629 ACTGGGTTTC


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

Matches are distributed among these distances:
  15   21  1.00

ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41


Consensus pattern (15 bp):   
CATCTTCATCATCAT

Found at i:615 original size:18 final size:18

Alignment explanation


    Indices: 592--626  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        582 GATCACGACA

                              
        592 TCATCATCATCATCTTCT
          1 TCATCATCATCATCTTCT

                             
        610 TCATCATCATCATCTTC
          1 TCATCATCATCATCTTC

        627 ATACTGGGTT


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:0.23, C:0.34, G:0.00, T:0.43


Consensus pattern (18 bp):   
TCATCATCATCATCTTCT
Done.