Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01833.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: 5167
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27


Found at i:4823 original size:45 final size:48

Alignment explanation


    Indices: 4754--4861  Score: 159
    Period size: 45  Copynumber: 2.2  Consensus size: 48

       4744 GCTTTCCCTG

                *                                           
       4754 GTGGTTGGGGTGCTTCTGGAACTGAAAGTGG-A-GG-TGGCAGCGGCA
          1 GTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAATGGATGGCAGCGGCA

                                                               
       4799 GTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCA
          1 GTGGCTGGGGTGCTTCTGGAACTGAAAGTGG-AATGG--ATGGCAGCGGCA

                        
       4850 GTGGCTGGGGTG
          1 GTGGCTGGGGTG

       4862 GCAGTGGCGG


Statistics
Matches: 56,  Mismatches: 1, Indels: 6
        0.89            0.02        0.10

Matches are distributed among these distances:
  45   30  0.54
  47    1  0.02
  48    2  0.04
  51   23  0.41

ACGTcount: A:0.19, C:0.14, G:0.46, T:0.21


Consensus pattern (48 bp):   
GTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAATGGATGGCAGCGGCA

Found at i:4864 original size:27 final size:27

Alignment explanation


    Indices: 4833--4888  Score: 76
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       4823 AAAGTGGAAA

                                       
       4833 TGGCAATGGCAGCGGCAGTGGCTGGGG
          1 TGGCAATGGCAGCGGCAGTGGCTGGGG

                 *    * *        *     
       4860 TGGCAGTGGCGGTGGCAGTGGTTGGGG
          1 TGGCAATGGCAGCGGCAGTGGCTGGGG

              
       4887 TG
          1 TG

       4889 CTTCTGGAAC


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.11, C:0.14, G:0.55, T:0.20


Consensus pattern (27 bp):   
TGGCAATGGCAGCGGCAGTGGCTGGGG

Found at i:4866 original size:15 final size:15

Alignment explanation


    Indices: 4846--4888  Score: 56
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       4836 CAATGGCAGC

                           
       4846 GGCAGTGGCTGGGGT
          1 GGCAGTGGCTGGGGT

                           
       4861 GGCAGTGGC---GGT
          1 GGCAGTGGCTGGGGT

                    *      
       4873 GGCAGTGGTTGGGGT
          1 GGCAGTGGCTGGGGT

             
       4888 G
          1 G

       4889 CTTCTGGAAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 6
        0.77            0.03        0.19

Matches are distributed among these distances:
  12   11  0.46
  15   13  0.54

ACGTcount: A:0.07, C:0.12, G:0.60, T:0.21


Consensus pattern (15 bp):   
GGCAGTGGCTGGGGT

Found at i:4915 original size:78 final size:78

Alignment explanation


    Indices: 4795--4941  Score: 258
    Period size: 78  Copynumber: 1.9  Consensus size: 78

       4785 AGGTGGCAGC

                                                                             
       4795 GGCAGTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCAGTGGCTGGGG
          1 GGCAGTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCAGTGGCTGGGG

                         
       4860 TGGCAGTGGCGGT
         66 TGGCAGTGGCGGT

                    *                           **                     *     
       4873 GGCAGTGGTTGGGGTGCTTCTGGAACTGAAAGTGGAGGTGGCAATGGCAGCGGCAGTGGTTGGGG
          1 GGCAGTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCAGTGGCTGGGG

                
       4938 TGGC
         66 TGGC

       4942 GGTAGTGGAG


Statistics
Matches: 65,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  78   65  1.00

ACGTcount: A:0.17, C:0.14, G:0.48, T:0.20


Consensus pattern (78 bp):   
GGCAGTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCAGTGGCTGGGG
TGGCAGTGGCGGT
Done.