Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g02459.F2

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: 4137
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:1477 original size:5 final size:6

Alignment explanation


    Indices: 1464--1521  Score: 80
    Period size: 6  Copynumber: 9.3  Consensus size: 6

       1454 ATAATTTAAT

                                     *      *                        
       1464 AAATAA AAATAA AAATCTAA AACTAA AACTAA AAATAA AAATAA AAATAA
          1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATAA AAATAA

                     
       1514 AAATAA AA
          1 AAATAA AA

       1522 CATATAATTT


Statistics
Matches: 48,  Mismatches: 2, Indels: 4
        0.89            0.04        0.07

Matches are distributed among these distances:
   6   43  0.90
   8    5  0.10

ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17


Consensus pattern (6 bp):   
AAATAA

Found at i:1585 original size:9 final size:9

Alignment explanation


    Indices: 1540--1598  Score: 64
    Period size: 9  Copynumber: 6.6  Consensus size: 9

       1530 TTTATACAAA

                   * 
       1540 TAATTCGGT
          1 TAATTCGAT

                 *  *
       1549 TAATTTGAG
          1 TAATTCGAT

                   **
       1558 TAATTCGGG
          1 TAATTCGAT

                 *   
       1567 TAATTTGAT
          1 TAATTCGAT

                     
       1576 TAATTCGAT
          1 TAATTCGAT

                     
       1585 TAATTCGAT
          1 TAATTCGAT

                 
       1594 TAATT
          1 TAATT

       1599 AAGTTTATTT


Statistics
Matches: 41,  Mismatches: 9, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
   9   41  1.00

ACGTcount: A:0.31, C:0.07, G:0.17, T:0.46


Consensus pattern (9 bp):   
TAATTCGAT

Found at i:1594 original size:18 final size:18

Alignment explanation


    Indices: 1540--1598  Score: 82
    Period size: 18  Copynumber: 3.3  Consensus size: 18

       1530 TTTATACAAA

                             *
       1540 TAATTCGGTTAATTTGAG
          1 TAATTCGGTTAATTTGAT

                    *         
       1558 TAATTCGGGTAATTTGAT
          1 TAATTCGGTTAATTTGAT

                   *      *   
       1576 TAATTCGATTAATTCGAT
          1 TAATTCGGTTAATTTGAT

                 
       1594 TAATT
          1 TAATT

       1599 AAGTTTATTT


Statistics
Matches: 36,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   36  1.00

ACGTcount: A:0.31, C:0.07, G:0.17, T:0.46


Consensus pattern (18 bp):   
TAATTCGGTTAATTTGAT
Done.