Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_07491

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: 4047
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23


Found at i:639 original size:6 final size:6

Alignment explanation


    Indices: 628--659  Score: 64
    Period size: 6  Copynumber: 5.3  Consensus size: 6

        618 GGTGCTTCCA

                                                 
        628 CAACAG CAACAG CAACAG CAACAG CAACAG CA
          1 CAACAG CAACAG CAACAG CAACAG CAACAG CA

        660 GCAGTTATAC


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

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.50, C:0.34, G:0.16, T:0.00


Consensus pattern (6 bp):   
CAACAG

Found at i:1206 original size:3 final size:3

Alignment explanation


    Indices: 1191--1227  Score: 65
    Period size: 3  Copynumber: 12.3  Consensus size: 3

       1181 TTCCAAATAT

                    *                                        
       1191 GCA GCA ACA GCA GCA GCA GCA GCA GCA GCA GCA GCA G
          1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA G

       1228 TTAATGGCTC


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.35, C:0.32, G:0.32, T:0.00


Consensus pattern (3 bp):   
GCA

Found at i:2593 original size:18 final size:18

Alignment explanation


    Indices: 2566--2635  Score: 61
    Period size: 18  Copynumber: 3.7  Consensus size: 18

       2556 GCTACTGCAA

                 *        *   
       2566 CAACAACAACAGCATCAG
          1 CAACAGCAACAGCAGCAG

                            *    
       2584 CAACAGCAACAACAGCGGCAG
          1 CAACAG---CAACAGCAGCAG

              *                
       2605 CAGCAGCAACAGCAGCAAG
          1 CAACAGCAACAGCAGC-AG

                         
       2624 CAA-AGCAACAGC
          1 CAACAGCAACAGC

       2636 TGTCCACTCA


Statistics
Matches: 42,  Mismatches: 6, Indels: 8
        0.75            0.11        0.14

Matches are distributed among these distances:
  18   23  0.55
  19    4  0.10
  21   15  0.36

ACGTcount: A:0.46, C:0.33, G:0.20, T:0.01


Consensus pattern (18 bp):   
CAACAGCAACAGCAGCAG

Found at i:2605 original size:21 final size:21

Alignment explanation


    Indices: 2562--2633  Score: 78
    Period size: 21  Copynumber: 3.6  Consensus size: 21

       2552 AGCAGCTACT

                  *           *  
       2562 GCAACAACAACAACAGCATCA
          1 GCAACAGCAACAACAGCAGCA

                             *   
       2583 GCAACAGCAACAACAGCGGCA
          1 GCAACAGCAACAACAGCAGCA

               *        *        
       2604 GCAGCAGCAACAGCAGCA--A
          1 GCAACAGCAACAACAGCAGCA

                        
       2623 GCAA-AGCAACA
          1 GCAACAGCAACA

       2634 GCTGTCCACT


Statistics
Matches: 44,  Mismatches: 7, Indels: 3
        0.81            0.13        0.06

Matches are distributed among these distances:
  18    7  0.16
  19    4  0.09
  21   33  0.75

ACGTcount: A:0.47, C:0.32, G:0.19, T:0.01


Consensus pattern (21 bp):   
GCAACAGCAACAACAGCAGCA
Done.