Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3591

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: 19967
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:476 original size:29 final size:29

Alignment explanation


    Indices: 439--494  Score: 85
    Period size: 29  Copynumber: 1.9  Consensus size: 29

        429 AGCGAGAGAT

                                         
        439 GCATCAAATGAATACTAAATATGAAGAAG
          1 GCATCAAATGAATACTAAATATGAAGAAG

                *     *     *          
        468 GCATGAAATGGATACTGAATATGAAGA
          1 GCATCAAATGAATACTAAATATGAAGA

        495 GGATGCGGAG


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  29   24  1.00

ACGTcount: A:0.48, C:0.09, G:0.21, T:0.21


Consensus pattern (29 bp):   
GCATCAAATGAATACTAAATATGAAGAAG

Found at i:9703 original size:29 final size:29

Alignment explanation


    Indices: 9666--9721  Score: 85
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       9656 AGCGAGAGAT

                                         
       9666 GCATCAAATGAATACTAAATATGAAGAAG
          1 GCATCAAATGAATACTAAATATGAAGAAG

                *     *     *          
       9695 GCATGAAATGGATACTGAATATGAAGA
          1 GCATCAAATGAATACTAAATATGAAGA

       9722 GGGATGCGGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  29   24  1.00

ACGTcount: A:0.48, C:0.09, G:0.21, T:0.21


Consensus pattern (29 bp):   
GCATCAAATGAATACTAAATATGAAGAAG

Found at i:19135 original size:18 final size:17

Alignment explanation


    Indices: 19112--19165  Score: 67
    Period size: 18  Copynumber: 3.2  Consensus size: 17

      19102 CCCAACTACT

                              
      19112 GTATACGTGAACAGTACC
          1 GTATACGTGAA-AGTACC

                           * 
      19130 GTATACGTGAAA-T-TC
          1 GTATACGTGAAAGTACC

                              
      19145 GTATACGTGAATAGTACC
          1 GTATACGTGAA-AGTACC

               
      19163 GTA
          1 GTA

      19166 AACGGTCGTA


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
  15   12  0.39
  16    2  0.06
  17    2  0.06
  18   15  0.48

ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28


Consensus pattern (17 bp):   
GTATACGTGAAAGTACC
Done.