Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_19090

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: 2475
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25


Found at i:1381 original size:3 final size:3

Alignment explanation


    Indices: 1373--1400  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       1363 AATTCTCCAT

                                                 
       1373 CAC CAC CAC CAC CAC CAC CAC CAC CAC C
          1 CAC CAC CAC CAC CAC CAC CAC CAC CAC C

       1401 TCCTCCTCCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00


Consensus pattern (3 bp):   
CAC

Found at i:1839 original size:6 final size:6

Alignment explanation


    Indices: 1828--1853  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

       1818 AGGTGGAGCA

                                          
       1828 CCACCT CCACCT CCACCT CCACCT CC
          1 CCACCT CCACCT CCACCT CCACCT CC

       1854 TGGAGGCCGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.15, C:0.69, G:0.00, T:0.15


Consensus pattern (6 bp):   
CCACCT

Found at i:1882 original size:36 final size:36

Alignment explanation


    Indices: 1837--1923  Score: 165
    Period size: 36  Copynumber: 2.4  Consensus size: 36

       1827 ACCACCTCCA

                                                
       1837 CCTCCACCTCCACCTCCTGGAGGCCGAGCTCCAGGC
          1 CCTCCACCTCCACCTCCTGGAGGCCGAGCTCCAGGC

                                           *    
       1873 CCTCCACCTCCACCTCCTGGAGGCCGAGCTCTAGGC
          1 CCTCCACCTCCACCTCCTGGAGGCCGAGCTCCAGGC

                           
       1909 CCTCCACCTCCACCT
          1 CCTCCACCTCCACCT

       1924 AGAGCTCCCG


Statistics
Matches: 50,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  36   50  1.00

ACGTcount: A:0.14, C:0.52, G:0.18, T:0.16


Consensus pattern (36 bp):   
CCTCCACCTCCACCTCCTGGAGGCCGAGCTCCAGGC
Done.