Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g01387.F1

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: 4304
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25


Found at i:1695 original size:6 final size:6

Alignment explanation


    Indices: 1686--1734  Score: 50
    Period size: 6  Copynumber: 8.7  Consensus size: 6

       1676 AAATAGTGCT

                       *       *      *                            
       1686 AGTGAC AGTGGC AGTGAT AGTGAT AGTGAC AGTGAC A--G-C AGTGAC
          1 AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC

                
       1731 AGTG
          1 AGTG

       1735 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:1701 original size:12 final size:12

Alignment explanation


    Indices: 1686--1747  Score: 52
    Period size: 12  Copynumber: 4.9  Consensus size: 12

       1676 AAATAGTGCT

                        
       1686 AGTGACAGTGGC
          1 AGTGACAGTGGC

                 *    **
       1698 AGTGATAGTGAT
          1 AGTGACAGTGGC

                           
       1710 AGTGACAGTGACAGC
          1 AGTGACAGTG---GC

                       *
       1725 AGTGACAGTGGA
          1 AGTGACAGTGGC

              *        
       1737 AGCGACAGTGG
          1 AGTGACAGTGG

       1748 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:1701 original size:18 final size:18

Alignment explanation


    Indices: 1680--1720  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       1670 GCAAGCAAAT

                *           * 
       1680 AGTGCTAGTGACAGTGGC
          1 AGTGATAGTGACAGTGAC

                       *      
       1698 AGTGATAGTGATAGTGAC
          1 AGTGATAGTGACAGTGAC

                 
       1716 AGTGA
          1 AGTGA

       1721 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.