Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g01335.P1

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: 3988
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38


Found at i:1510 original size:6 final size:6

Alignment explanation


    Indices: 1499--1538  Score: 53
    Period size: 6  Copynumber: 6.7  Consensus size: 6

       1489 CTTTTTATAT

                                     *       *     *      
       1499 TTTTAA TTTTAA TTTTAA TTTTGA TTTTAT TTTTTA TTTT
          1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT

       1539 TATAATTTTA


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75


Consensus pattern (6 bp):   
TTTTAA

Found at i:1630 original size:14 final size:14

Alignment explanation


    Indices: 1584--1627  Score: 56
    Period size: 13  Copynumber: 3.3  Consensus size: 14

       1574 TACTATGTTA

                          
       1584 AATTATATTTTTAT
          1 AATTATATTTTTAT

                          
       1598 AATTAT-TTTTTAT
          1 AATTATATTTTTAT

             *  *         
       1611 -TTTTTATTTTTAT
          1 AATTATATTTTTAT

                
       1624 AATT
          1 AATT

       1628 TTAAATTTAG


Statistics
Matches: 25,  Mismatches: 3, Indels: 4
        0.78            0.09        0.12

Matches are distributed among these distances:
  12    3  0.12
  13   14  0.56
  14    8  0.32

ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70


Consensus pattern (14 bp):   
AATTATATTTTTAT

Found at i:2016 original size:27 final size:28

Alignment explanation


    Indices: 1986--2042  Score: 80
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       1976 TTGAGTTATT

                                        
       1986 AATTCATT-ATTTTAAAATTTAAATTTA
          1 AATTCATTAATTTTAAAATTTAAATTTA

                          * *      *    
       2013 AATTCATTAATTTTTATATTTAATTTTA
          1 AATTCATTAATTTTAAAATTTAAATTTA

              
       2041 AA
          1 AA

       2043 GTTAAAATTT


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  27    8  0.31
  28   18  0.69

ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54


Consensus pattern (28 bp):   
AATTCATTAATTTTAAAATTTAAATTTA

Found at i:2035 original size:35 final size:34

Alignment explanation


    Indices: 1983--2048  Score: 80
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       1973 TAATTGAGTT

                                      *        
       1983 ATTAATTCATTATTTTAAAATTTAAATTTAAATTC
          1 ATTAATTCATTATTTT-AAATTTAAAGTTAAATTC

                    *          *            
       2018 ATTAATT-TTTATATTTAATTTTAAAGTTAAA
          1 ATTAATTCATTAT-TTTAAATTTAAAGTTAAA

       2049 ATTTTCATAG


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  34   17  0.63
  35   10  0.37

ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53


Consensus pattern (34 bp):   
ATTAATTCATTATTTTAAATTTAAAGTTAAATTC
Done.