Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g01847.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: 3740
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31


Found at i:2049 original size:28 final size:28

Alignment explanation


    Indices: 2009--2065  Score: 114
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       1999 GCTTAAAGAA

                                        
       2009 GAAAATGTTGAAGAATGGTTGTGAAATT
          1 GAAAATGTTGAAGAATGGTTGTGAAATT

                                        
       2037 GAAAATGTTGAAGAATGGTTGTGAAATT
          1 GAAAATGTTGAAGAATGGTTGTGAAATT

             
       2065 G
          1 G

       2066 CAAGTACATT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   29  1.00

ACGTcount: A:0.39, C:0.00, G:0.30, T:0.32


Consensus pattern (28 bp):   
GAAAATGTTGAAGAATGGTTGTGAAATT

Found at i:2781 original size:39 final size:39

Alignment explanation


    Indices: 2727--2878  Score: 243
    Period size: 39  Copynumber: 3.9  Consensus size: 39

       2717 GAATGTTCGA

                                                *  
       2727 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATT
          1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT

                                                 * 
       2766 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
          1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT

            *                                      
       2805 ATGATATCCGGGCTAAG-CCGAAGGCAATTGTGCGAGTT
          1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT

                        *               *       
       2843 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
          1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG

       2879 GGTTACCATA


Statistics
Matches: 104,  Mismatches: 7, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  38   35  0.34
  39   53  0.51
  40   16  0.15

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


Consensus pattern (39 bp):   
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT

Found at i:2839 original size:77 final size:79

Alignment explanation


    Indices: 2728--2878  Score: 261
    Period size: 77  Copynumber: 1.9  Consensus size: 79

       2718 AATGTTCGAG

                                                                             
       2728 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGC
          1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTGTGATATCCGGGCTAAGTCCCGAAGGC

                          
       2792 AATTGTGCGAGCTA
         66 AATTGTGCGAGCTA

                                               *              *              
       2806 TGATATCCGGGCTAAG-CCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGC
          1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTGTGATATCCGGGCTAAGTCCCGAAGGC

             *       
       2870 ATTTGTGCG
         66 AATTGTGCG

       2879 GGTTACCATA


Statistics
Matches: 69,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  77   36  0.52
  78   33  0.48

ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24


Consensus pattern (79 bp):   
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGCTA

Found at i:2894 original size:40 final size:39

Alignment explanation


    Indices: 2728--2908  Score: 238
    Period size: 39  Copynumber: 4.6  Consensus size: 39

       2718 AATGTTCGAG

                                               *  *
       2728 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTG
          1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA

                                                *  
       2767 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
          1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA

                                                  *
       2806 TGATATCCGGGCTAAG-CCGAAGGCAATTGTGCGAGTTG
          1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA

                       *               *       *    
       2844 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
          1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA

            **   *        *          
       2884 CCATAACCGGGCTATGTCCCGAAGG
          1 TGATATCCGGGCTAAG-CCCGAAGG

       2909 TGTTTTGAAC


Statistics
Matches: 126,  Mismatches: 14, Indels: 3
        0.88            0.10        0.02

Matches are distributed among these distances:
  38   35  0.28
  39   52  0.41
  40   39  0.31

ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23


Consensus pattern (39 bp):   
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA

Done.