Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2600

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, 540

Length: 901
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36


Found at i:162 original size:43 final size:42

Alignment explanation


    Indices: 1--179  Score: 277
    Period size: 42  Copynumber: 4.2  Consensus size: 42

                                *                    * 
          1 GCGTTTTCTTCCCAAGCGCCACTAAAGAACATGATCTTTAGTG
          1 GCGTTTT-TTCCCAAGCGCCGCTAAAGAACATGATCTTTAGCG

                             *                        
         44 GCGTTTTTTCCCAAGCGACGCTAAAGAACATGATCTTTAGCG
          1 GCGTTTTTTCCCAAGCGCCGCTAAAGAACATGATCTTTAGCG

                                *                    *
         86 GCGTTTTTTCCCAAGCGCCGTTAAAGAACATGATCTTTAGCA
          1 GCGTTTTTTCCCAAGCGCCGCTAAAGAACATGATCTTTAGCG

                        *                *             
        128 GCGTTTTCTTCCTAAGCGCCGCTAAAGAATATGATCTTTAGCG
          1 GCGTTTT-TTCCCAAGCGCCGCTAAAGAACATGATCTTTAGCG

                     
        171 GCGTTTTTT
          1 GCGTTTTTT

        180 TCTGTAAGCA


Statistics
Matches: 125,  Mismatches: 10, Indels: 3
        0.91            0.07        0.02

Matches are distributed among these distances:
  42   80  0.64
  43   45  0.36

ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32


Consensus pattern (42 bp):   
GCGTTTTTTCCCAAGCGCCGCTAAAGAACATGATCTTTAGCG

Found at i:178 original size:84 final size:84

Alignment explanation


    Indices: 1--179  Score: 277
    Period size: 85  Copynumber: 2.1  Consensus size: 84

                                                     **                      
          1 GCGTTTTCTTCCCAAGCGCCACTAAAGAACATGATCTTTAGTGGCGTTTTTTCCCAAGCGACGCT
          1 GCGTTTT-TTCCCAAGCGCCACTAAAGAACATGATCTTTAGCAGCGTTTTTTCCCAAGCGACGCT

                                
         66 AAAGAACATGATCTTTAGCG
         65 AAAGAACATGATCTTTAGCG

                               **                                 *     *    
         86 GCGTTTTTTCCCAAGCGCCGTTAAAGAACATGATCTTTAGCAGCGTTTTCTTCCTAAGCGCCGCT
          1 GCGTTTTTTCCCAAGCGCCACTAAAGAACATGATCTTTAGCAGCGTTTT-TTCCCAAGCGACGCT

                  *             
        151 AAAGAATATGATCTTTAGCG
         65 AAAGAACATGATCTTTAGCG

                     
        171 GCGTTTTTT
          1 GCGTTTTTT

        180 TCTGTAAGCA


Statistics
Matches: 86,  Mismatches: 7, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  84   38  0.44
  85   48  0.56

ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32


Consensus pattern (84 bp):   
GCGTTTTTTCCCAAGCGCCACTAAAGAACATGATCTTTAGCAGCGTTTTTTCCCAAGCGACGCTA
AAGAACATGATCTTTAGCG

Found at i:235 original size:15 final size:15

Alignment explanation


    Indices: 198--236  Score: 69
    Period size: 15  Copynumber: 2.6  Consensus size: 15

        188 CACCGCAAAA

                   *       
        198 GTTAGCGACGTTGTC
          1 GTTAGCGGCGTTGTC

                           
        213 GTTAGCGGCGTTGTC
          1 GTTAGCGGCGTTGTC

                     
        228 GTTAGCGGC
          1 GTTAGCGGC

        237 ATTTTTTGTG


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.10, C:0.21, G:0.38, T:0.31


Consensus pattern (15 bp):   
GTTAGCGGCGTTGTC
Done.