Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_24495

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, 687

Length: 1145
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20


Found at i:476 original size:21 final size:21

Alignment explanation


    Indices: 450--496  Score: 94
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        440 TGCACCGTCT

                                 
        450 CCTCCACCATCACAGCCGCTG
          1 CCTCCACCATCACAGCCGCTG

                                 
        471 CCTCCACCATCACAGCCGCTG
          1 CCTCCACCATCACAGCCGCTG

                 
        492 CCTCC
          1 CCTCC

        497 GCCACCGCAG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.17, C:0.55, G:0.13, T:0.15


Consensus pattern (21 bp):   
CCTCCACCATCACAGCCGCTG

Found at i:507 original size:21 final size:21

Alignment explanation


    Indices: 450--513  Score: 83
    Period size: 21  Copynumber: 3.0  Consensus size: 21

        440 TGCACCGTCT

                     *           
        450 CCTCCACCATCACAGCCGCTG
          1 CCTCCACCACCACAGCCGCTG

                     *           
        471 CCTCCACCATCACAGCCGCTG
          1 CCTCCACCACCACAGCCGCTG

                 *     *    *    
        492 CCTCCGCCACCGCAGCAGCTG
          1 CCTCCACCACCACAGCCGCTG

             
        513 C
          1 C

        514 ATCTGACAGC


Statistics
Matches: 39,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   39  1.00

ACGTcount: A:0.17, C:0.53, G:0.17, T:0.12


Consensus pattern (21 bp):   
CCTCCACCACCACAGCCGCTG

Found at i:612 original size:3 final size:3

Alignment explanation


    Indices: 606--630  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

        596 GGTGGTGCTG

                                             
        606 CAA CAA CAA CAA CAA CAA CAA CAA C
          1 CAA CAA CAA CAA CAA CAA CAA CAA C

        631 CACCACCGCC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00


Consensus pattern (3 bp):   
CAA

Done.