Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold327

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: 596179
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


File 5 of 5

Found at i:589871 original size:27 final size:28

Alignment explanation


    Indices: 589810--589883  Score: 98
    Period size: 27  Copynumber: 2.7  Consensus size: 28

     589800 AATAAAGTCA

                             *           
     589810 GGGTTGGAGTATCCCCTCA-GAAATAACG
          1 GGGTTGGAGTATCCCC-GATGAAATAACG

                                  *     
     589838 GGGTTGGAGTATCCCCGATG-ATTAACG
          1 GGGTTGGAGTATCCCCGATGAAATAACG

                      *        
     589865 GGGTTGGAGTGTCCCCGAT
          1 GGGTTGGAGTATCCCCGAT

     589884 TGTGAAGAAA


Statistics
Matches: 42,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
  27   25  0.60
  28   17  0.40

ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24


Consensus pattern (28 bp):   
GGGTTGGAGTATCCCCGATGAAATAACG

Found at i:594939 original size:24 final size:23

Alignment explanation


    Indices: 594912--594977  Score: 71
    Period size: 24  Copynumber: 2.8  Consensus size: 23

     594902 TGGTGTGAAA

                            *       
     594912 GGGGGGGGGAGGGGCGGGGGACGG
          1 GGGGGGGGGAGGGGCGAGGGA-GG

                           *        
     594936 GGGGGGGGG-GGTGGTGAGGGAGG
          1 GGGGGGGGGAGG-GGCGAGGGAGG

                 *       *     
     594959 GGGGGTGGGAGGGCCGAGG
          1 GGGGGGGGGAGGGGCGAGG

     594978 AGAAGTTGAA


Statistics
Matches: 35,  Mismatches: 5, Indels: 5
        0.78            0.11        0.11

Matches are distributed among these distances:
  23   17  0.49
  24   18  0.51

ACGTcount: A:0.09, C:0.06, G:0.80, T:0.05


Consensus pattern (23 bp):   
GGGGGGGGGAGGGGCGAGGGAGG

Found at i:594960 original size:17 final size:16

Alignment explanation


    Indices: 594912--594971  Score: 56
    Period size: 16  Copynumber: 3.9  Consensus size: 16

     594902 TGGTGTGAAA

                            
     594912 GGGGGG-GGGAGGG-G
          1 GGGGGGTGGGAGGGAG

                  **         
     594926 CGGGGGACGGG-GGG-G
          1 -GGGGGGTGGGAGGGAG

                             
     594941 GGGGGGTGGTGAGGGAG
          1 GGGGGGTGG-GAGGGAG

                          
     594958 GGGGGGTGGGAGGG
          1 GGGGGGTGGGAGGG

     594972 CCGAGGAGAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 7
        0.79            0.06        0.15

Matches are distributed among these distances:
  14    7  0.18
  15   10  0.26
  16   11  0.29
  17   10  0.26

ACGTcount: A:0.08, C:0.03, G:0.83, T:0.05


Consensus pattern (16 bp):   
GGGGGGTGGGAGGGAG

Found at i:594977 original size:23 final size:23

Alignment explanation


    Indices: 594912--594977  Score: 71
    Period size: 23  Copynumber: 2.8  Consensus size: 23

     594902 TGGTGTGAAA

                            *      
     594912 GGGGGGGGGAGGGGCGGGGGACG
          1 GGGGGGGGGAGGGGCGAGGGACG

                     *     *        
     594935 GGGGGGGGGGGGTGGTGAGGGA-G
          1 GGGGGGGGGAGG-GGCGAGGGACG

                          *     
     594958 GGGGGGTGGGAGGGCCGAGG
          1 GGGGGG-GGGAGGGGCGAGG

     594978 AGAAGTTGAA


Statistics
Matches: 35,  Mismatches: 6, Indels: 4
        0.78            0.13        0.09

Matches are distributed among these distances:
  23   23  0.66
  24   12  0.34

ACGTcount: A:0.09, C:0.06, G:0.80, T:0.05


Consensus pattern (23 bp):   
GGGGGGGGGAGGGGCGAGGGACG

Done.