Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_32263

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, 432

Length: 720
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23


Found at i:543 original size:15 final size:15

Alignment explanation


    Indices: 523--572  Score: 61
    Period size: 15  Copynumber: 3.5  Consensus size: 15

        513 GAAGCCAGAT

                           
        523 CACCATGACCACGAG
          1 CACCATGACCACGAG

                    **     
        538 CACCATGATGA--AG
          1 CACCATGACCACGAG

                           
        551 -ACCATGACCACGAG
          1 CACCATGACCACGAG

                    
        565 CACCATGA
          1 CACCATGA

        573 TGAAGAGGAT


Statistics
Matches: 28,  Mismatches: 4, Indels: 6
        0.74            0.11        0.16

Matches are distributed among these distances:
  12    8  0.29
  13    2  0.07
  14    2  0.07
  15   16  0.57

ACGTcount: A:0.36, C:0.34, G:0.20, T:0.10


Consensus pattern (15 bp):   
CACCATGACCACGAG

Found at i:554 original size:27 final size:27

Alignment explanation


    Indices: 524--578  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        514 AAGCCAGATC

                                       
        524 ACCATGACCACGAGCACCATGATGAAG
          1 ACCATGACCACGAGCACCATGATGAAG

                                       
        551 ACCATGACCACGAGCACCATGATGAAG
          1 ACCATGACCACGAGCACCATGATGAAG

             
        578 A
          1 A

        579 GGATCATGAG


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

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.38, C:0.29, G:0.22, T:0.11


Consensus pattern (27 bp):   
ACCATGACCACGAGCACCATGATGAAG

Found at i:624 original size:15 final size:15

Alignment explanation


    Indices: 604--637  Score: 59
    Period size: 15  Copynumber: 2.3  Consensus size: 15

        594 GCATCACCAC

                           
        604 CACCACCACCATCAT
          1 CACCACCACCATCAT

                   *       
        619 CACCACCGCCATCAT
          1 CACCACCACCATCAT

                
        634 CACC
          1 CACC

        638 GTGGAGAGGA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.29, C:0.56, G:0.03, T:0.12


Consensus pattern (15 bp):   
CACCACCACCATCAT
Done.