Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01078.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: 2762
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30


Found at i:1904 original size:17 final size:17

Alignment explanation


    Indices: 1879--1914  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       1869 AAGTTGACTT

                *     *      
       1879 GAACTTAAAACCAATTC
          1 GAACATAAAAACAATTC

                             
       1896 GAACATAAAAACAATTC
          1 GAACATAAAAACAATTC

              
       1913 GA
          1 GA

       1915 CCAAGTTAAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.53, C:0.19, G:0.08, T:0.19


Consensus pattern (17 bp):   
GAACATAAAAACAATTC

Found at i:1938 original size:48 final size:48

Alignment explanation


    Indices: 1867--1962  Score: 147
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       1857 CAACCCATAC

                   *                   * *    *             
       1867 CCAAGTTGACTTGAACTTAAAACCAATTCGAACATAAAAACAATTCGA
          1 CCAAGTTAACTTGAACTTAAAACCAATCCAAACACAAAAACAATTCGA

                                             *              
       1915 CCAAGTTAACTTGAACTTAAAACCAATCCAAACCCAAAAACAATTCGA
          1 CCAAGTTAACTTGAACTTAAAACCAATCCAAACACAAAAACAATTCGA

       1963 AAGTAATTTA


Statistics
Matches: 43,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  48   43  1.00

ACGTcount: A:0.47, C:0.24, G:0.08, T:0.21


Consensus pattern (48 bp):   
CCAAGTTAACTTGAACTTAAAACCAATCCAAACACAAAAACAATTCGA

Found at i:2043 original size:11 final size:12

Alignment explanation


    Indices: 2010--2046  Score: 67
    Period size: 12  Copynumber: 3.2  Consensus size: 12

       2000 CTCGAAATTG

                        
       2010 ACCGAATCCTTC
          1 ACCGAATCCTTC

                        
       2022 ACCGAATCCTTC
          1 ACCGAATCCTTC

                        
       2034 ACCG-ATCCTTC
          1 ACCGAATCCTTC

              
       2045 AC
          1 AC

       2047 GGAAATCTTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  11    9  0.36
  12   16  0.64

ACGTcount: A:0.24, C:0.43, G:0.08, T:0.24


Consensus pattern (12 bp):   
ACCGAATCCTTC
Done.