Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00287.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: 4117
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:75 original size:17 final size:18

Alignment explanation


    Indices: 44--77  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

         34 AATTCACGCT

                              
         44 TTTTGACCTTAAATTTAC
          1 TTTTGACCTTAAATTTAC

                      *      
         62 TTTTG-CCTTCAATTTA
          1 TTTTGACCTTAAATTTA

         78 GTCCCTAAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17   10  0.67
  18    5  0.33

ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53


Consensus pattern (18 bp):   
TTTTGACCTTAAATTTAC

Found at i:673 original size:99 final size:99

Alignment explanation


    Indices: 502--700  Score: 274
    Period size: 99  Copynumber: 2.0  Consensus size: 99

        492 TAATTTATTT

                                   *    *                                    
        502 ATTTATTTATTTTTGCTTAAGAATATATTGAACATTTTGACGCAAAGAAAAATAACAACCAAGCA
          1 ATTTATTTATTTTTGCTTAAGAACATATCGAACATTTTGACGCAAAGAAAAATAACAACCAAGCA

                                              
        567 CCCCACCCCGGTTACTCAGCCCAACATACTCCTA
         66 CCCCACCCCGGTTACTCAGCCCAACATACTCCTA

                                              *         *    * *  *   *      
        601 ATTTATTATATTTTT-CTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGC
          1 ATTTATT-TATTTTTGCTTAAGAACATATCGAACATTTTGACGCAAAGAAAAATAACAACCAAGC

               *                 *   *   *     
        665 ACCTCACCCCGGTTACTCAGCGCAATATATTCCTA
         65 ACCCCACCCCGGTTACTCAGCCCAACATACTCCTA

             
        700 A
          1 A

        701 AAAAATTATT


Statistics
Matches: 87,  Mismatches: 12, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  99   80  0.92
 100    7  0.08

ACGTcount: A:0.34, C:0.25, G:0.13, T:0.29


Consensus pattern (99 bp):   
ATTTATTTATTTTTGCTTAAGAACATATCGAACATTTTGACGCAAAGAAAAATAACAACCAAGCA
CCCCACCCCGGTTACTCAGCCCAACATACTCCTA

Found at i:1837 original size:18 final size:18

Alignment explanation


    Indices: 1793--1837  Score: 56
    Period size: 18  Copynumber: 2.5  Consensus size: 18

       1783 ATATCCCAAA

                   *  *       
       1793 AATAAAATAATAAATAAT
          1 AATAAAAAAAGAAATAAT

                               
       1811 AA-AAGAAAAAGAAATAAT
          1 AATAA-AAAAAGAAATAAT

                     
       1829 AATAAAAAA
          1 AATAAAAAA

       1838 TAAAAATTGG


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  17    2  0.09
  18   19  0.83
  19    2  0.09

ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18


Consensus pattern (18 bp):   
AATAAAAAAAGAAATAAT
Done.