Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_05425

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: 3558
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24


Found at i:1501 original size:6 final size:6

Alignment explanation


    Indices: 1492--1540  Score: 50
    Period size: 6  Copynumber: 8.7  Consensus size: 6

       1482 AAATAGTGCT

                       *       *      *                            
       1492 AGTGAC AGTGGC AGTGAT AGTGAT AGTGAC AGTGAC A--G-C AGTGAC
          1 AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC

                
       1537 AGTG
          1 AGTG

       1541 GAAGCGACAG


Statistics
Matches: 36,  Mismatches: 4, Indels: 6
        0.78            0.09        0.13

Matches are distributed among these distances:
   3    2  0.06
   4    1  0.03
   5    1  0.03
   6   32  0.89

ACGTcount: A:0.31, C:0.12, G:0.37, T:0.20


Consensus pattern (6 bp):   
AGTGAC

Found at i:1507 original size:12 final size:12

Alignment explanation


    Indices: 1492--1553  Score: 52
    Period size: 12  Copynumber: 4.9  Consensus size: 12

       1482 AAATAGTGCT

                        
       1492 AGTGACAGTGGC
          1 AGTGACAGTGGC

                 *    **
       1504 AGTGATAGTGAT
          1 AGTGACAGTGGC

                           
       1516 AGTGACAGTGACAGC
          1 AGTGACAGTG---GC

                       *
       1531 AGTGACAGTGGA
          1 AGTGACAGTGGC

              *        
       1543 AGCGACAGTGG
          1 AGTGACAGTGG

       1554 AAGCCACAGC


Statistics
Matches: 39,  Mismatches: 8, Indels: 6
        0.74            0.15        0.11

Matches are distributed among these distances:
  12   29  0.74
  15   10  0.26

ACGTcount: A:0.31, C:0.13, G:0.39, T:0.18


Consensus pattern (12 bp):   
AGTGACAGTGGC

Found at i:1507 original size:18 final size:18

Alignment explanation


    Indices: 1486--1526  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       1476 GCAAGCAAAT

                *           * 
       1486 AGTGCTAGTGACAGTGGC
          1 AGTGATAGTGACAGTGAC

                       *      
       1504 AGTGATAGTGATAGTGAC
          1 AGTGATAGTGACAGTGAC

                 
       1522 AGTGA
          1 AGTGA

       1527 CAGCAGTGAC


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.29, C:0.10, G:0.37, T:0.24


Consensus pattern (18 bp):   
AGTGATAGTGACAGTGAC
Done.