Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_103 ID=scaffold_103-JGI_221_v2.0

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: 13793
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.30

Warning! 100 characters in sequence are not A, C, G, or T


Found at i:2700 original size:42 final size:42

Alignment explanation


    Indices: 2639--2721  Score: 157
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       2629 AATATGTGTG

                                                      
       2639 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
          1 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA

                          *                          
       2681 AAACGTTTGAAATTGAAACATTTGAACTCTTGTTCTTATCC
          1 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC

       2722 CTTTGAATTT


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39


Consensus pattern (42 bp):   
AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA

Found at i:9142 original size:42 final size:42

Alignment explanation


    Indices: 9095--9177  Score: 157
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       9085 AATATGTGTG

                                                      
       9095 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA
          1 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA

                          *                          
       9137 AAACGTTTGAAATTGAAACATTTGAACTCTTGTTCTTATCC
          1 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC

       9178 CTTTGAATTT


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39


Consensus pattern (42 bp):   
AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCA

Found at i:9393 original size:15 final size:15

Alignment explanation


    Indices: 9372--9418  Score: 53
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       9362 TGAGCTGGTA

                            
       9372 GAGCTGAAATTGAGCT
          1 GAGCTGAAA-TGAGCT

                             
       9388 -AGCTGAAAATGTA-CT
          1 GAGCTG-AAATG-AGCT

                           
       9403 GAGCTGAAATGAGCT
          1 GAGCTGAAATGAGCT

             
       9418 G
          1 G

       9419 GAAACGAACT


Statistics
Matches: 27,  Mismatches: 0, Indels: 9
        0.75            0.00        0.25

Matches are distributed among these distances:
  14    1  0.04
  15   17  0.63
  16    9  0.33

ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23


Consensus pattern (15 bp):   
GAGCTGAAATGAGCT
Done.