Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: evm.model.Ga06G2144

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: 4935
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26


Found at i:4721 original size:45 final size:48

Alignment explanation


    Indices: 4652--4759  Score: 159
    Period size: 45  Copynumber: 2.2  Consensus size: 48

       4642 GCTTTCCCTG

                *                                           
       4652 GTGGTTGGGGTGCTTCTGGAACTGAAAGTGG-A-GG-TGGCAGCGGCA
          1 GTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAATGGATGGCAGCGGCA

                                                               
       4697 GTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCA
          1 GTGGCTGGGGTGCTTCTGGAACTGAAAGTGG-AATGG--ATGGCAGCGGCA

                        
       4748 GTGGCTGGGGTG
          1 GTGGCTGGGGTG

       4760 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:4762 original size:27 final size:27

Alignment explanation


    Indices: 4731--4786  Score: 76
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       4721 AAAGTGGAAA

                                       
       4731 TGGCAATGGCAGCGGCAGTGGCTGGGG
          1 TGGCAATGGCAGCGGCAGTGGCTGGGG

                 *    * *        *     
       4758 TGGCAGTGGCGGTGGCAGTGGTTGGGG
          1 TGGCAATGGCAGCGGCAGTGGCTGGGG

              
       4785 TG
          1 TG

       4787 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:4764 original size:15 final size:15

Alignment explanation


    Indices: 4744--4786  Score: 56
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       4734 CAATGGCAGC

                           
       4744 GGCAGTGGCTGGGGT
          1 GGCAGTGGCTGGGGT

                           
       4759 GGCAGTGGC---GGT
          1 GGCAGTGGCTGGGGT

                    *      
       4771 GGCAGTGGTTGGGGT
          1 GGCAGTGGCTGGGGT

             
       4786 G
          1 G

       4787 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:4813 original size:78 final size:78

Alignment explanation


    Indices: 4693--4839  Score: 258
    Period size: 78  Copynumber: 1.9  Consensus size: 78

       4683 AGGTGGCAGC

                                                                             
       4693 GGCAGTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCAGTGGCTGGGG
          1 GGCAGTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCAGTGGCTGGGG

                         
       4758 TGGCAGTGGCGGT
         66 TGGCAGTGGCGGT

                    *                           **                     *     
       4771 GGCAGTGGTTGGGGTGCTTCTGGAACTGAAAGTGGAGGTGGCAATGGCAGCGGCAGTGGTTGGGG
          1 GGCAGTGGCTGGGGTGCTTCTGGAACTGAAAGTGGAAATGGCAATGGCAGCGGCAGTGGCTGGGG

                
       4836 TGGC
         66 TGGC

       4840 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.