Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_226 ID=scaffold_226-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: 9280
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32

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


Found at i:720 original size:32 final size:32

Alignment explanation


    Indices: 667--727  Score: 88
    Period size: 32  Copynumber: 1.9  Consensus size: 32

        657 TTGGGGCTTC

                      *    *                
        667 TTAAAAGAGTTTAATTAAATTTTCAAAAAAAA
          1 TTAAAAGAGTATAATGAAATTTTCAAAAAAAA

                                          
        699 TTAAAAG-GTATAATGAGAATTTTCAAAAA
          1 TTAAAAGAGTATAATGA-AATTTTCAAAAA

        728 TTTGGGACCT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  31    7  0.27
  32   19  0.73

ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33


Consensus pattern (32 bp):   
TTAAAAGAGTATAATGAAATTTTCAAAAAAAA

Found at i:1315 original size:4 final size:4

Alignment explanation


    Indices: 1306--1354  Score: 98
    Period size: 4  Copynumber: 12.2  Consensus size: 4

       1296 TGCTTGCACG

                                                                       
       1306 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
          1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA

             
       1354 C
          1 C

       1355 CTGGATGATG


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   45  1.00

ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24


Consensus pattern (4 bp):   
CATA

Found at i:2025 original size:28 final size:31

Alignment explanation


    Indices: 1984--2041  Score: 86
    Period size: 28  Copynumber: 2.0  Consensus size: 31

       1974 ATCTTAAATA

                          *                
       1984 ATTATAAAAAATTATTAAA-C-AATATTTAT
          1 ATTATAAAAAATTAATAAAGCGAATATTTAT

                                          
       2013 ATTA-AAAAAATTAATAAAGCGAATATTTA
          1 ATTATAAAAAATTAATAAAGCGAATATTTA

       2042 AAAAATTGAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  28   13  0.50
  29    5  0.19
  30    8  0.31

ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36


Consensus pattern (31 bp):   
ATTATAAAAAATTAATAAAGCGAATATTTAT

Found at i:2068 original size:15 final size:15

Alignment explanation


    Indices: 2048--2076  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       2038 TTTAAAAAAT

                           
       2048 TGAATTAAATAAAGG
          1 TGAATTAAATAAAGG

                          
       2063 TGAATTAAATAAAG
          1 TGAATTAAATAAAG

       2077 AATGAAAGCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28


Consensus pattern (15 bp):   
TGAATTAAATAAAGG
Done.