Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_07579

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, 651

Length: 1086
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19


Found at i:209 original size:33 final size:33

Alignment explanation


    Indices: 172--323  Score: 156
    Period size: 33  Copynumber: 4.8  Consensus size: 33

        162 ATTCCAGCCA

                 *                           
        172 CAACAACCACCGCAATACCCACCACCTGCTCAG
          1 CAACAGCCACCGCAATACCCACCACCTGCTCAG

                                             
        205 CAACAGCCA-CG----A-CCACCACCTGCTCAG
          1 CAACAGCCACCGCAATACCCACCACCTGCTCAG

                      *                     *
        232 CAACAGCCACGGCAATACCCACCACCTGCTCAA
          1 CAACAGCCACCGCAATACCCACCACCTGCTCAG

              *     *     *       *           
        265 CAGCAGCCTCCGCAGTACCCACTACCTGCTCTA-
          1 CAACAGCCACCGCAATACCCACCACCTGCTC-AG

              *     *     *           
        298 CAGCAGCCTCCGCAGTACCCACCACC
          1 CAACAGCCACCGCAATACCCACCACC

        324 ATCACAACAA


Statistics
Matches: 103,  Mismatches: 9, Indels: 14
        0.82            0.07        0.11

Matches are distributed among these distances:
  27   24  0.23
  28    2  0.02
  32    3  0.03
  33   73  0.71
  34    1  0.01

ACGTcount: A:0.28, C:0.48, G:0.13, T:0.11


Consensus pattern (33 bp):   
CAACAGCCACCGCAATACCCACCACCTGCTCAG

Found at i:227 original size:27 final size:27

Alignment explanation


    Indices: 190--242  Score: 106
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        180 ACCGCAATAC

                                       
        190 CCACCACCTGCTCAGCAACAGCCACGA
          1 CCACCACCTGCTCAGCAACAGCCACGA

                                      
        217 CCACCACCTGCTCAGCAACAGCCACG
          1 CCACCACCTGCTCAGCAACAGCCACG

        243 GCAATACCCA


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

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.28, C:0.49, G:0.15, T:0.08


Consensus pattern (27 bp):   
CCACCACCTGCTCAGCAACAGCCACGA
Done.