Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00121.F1

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: 4502
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32


Found at i:1046 original size:55 final size:55

Alignment explanation


    Indices: 977--1086  Score: 193
    Period size: 55  Copynumber: 2.0  Consensus size: 55

        967 TAATTCTTCA

                                   **                              
        977 TTAAAAATTCTATCAATTTCTACGGTTGAAAAACTAGTTTTTATACATCAATAGG
          1 TTAAAAATTCTATCAATTTCTACAATTGAAAAACTAGTTTTTATACATCAATAGG

                     *                                             
       1032 TTAAAAATTTTATCAATTTCTACAATTGAAAAACTAGTTTTTATACATCAATAGG
          1 TTAAAAATTCTATCAATTTCTACAATTGAAAAACTAGTTTTTATACATCAATAGG

       1087 AGATATACGT


Statistics
Matches: 52,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  55   52  1.00

ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39


Consensus pattern (55 bp):   
TTAAAAATTCTATCAATTTCTACAATTGAAAAACTAGTTTTTATACATCAATAGG

Found at i:3678 original size:41 final size:41

Alignment explanation


    Indices: 3612--3737  Score: 185
    Period size: 35  Copynumber: 3.2  Consensus size: 41

       3602 TTCTTACTAA

                                        *            
       3612 ATGAGATATTTAT-ACAAGCATACAAATATAAGTGTATTAT
          1 ATGAGATATTTATCACAAGCATACAAATCTAAGTGTATTAT

                                                     
       3652 ATGAGATATTTATCACAAGCATACAAATCTAA--G---T-T
          1 ATGAGATATTTATCACAAGCATACAAATCTAAGTGTATTAT

                           *                         
       3687 ATGAGATATTTATCAGAAGCATACAAATCTAAGTGTATTAT
          1 ATGAGATATTTATCACAAGCATACAAATCTAAGTGTATTAT

                      
       3728 ATGAGATATT
          1 ATGAGATATT

       3738 ATGATTTAGT


Statistics
Matches: 77,  Mismatches: 2, Indels: 13
        0.84            0.02        0.14

Matches are distributed among these distances:
  35   32  0.42
  36    1  0.01
  37    1  0.01
  39    1  0.01
  40   14  0.18
  41   28  0.36

ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34


Consensus pattern (41 bp):   
ATGAGATATTTATCACAAGCATACAAATCTAAGTGTATTAT

Found at i:4121 original size:31 final size:31

Alignment explanation


    Indices: 4081--4152  Score: 92
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       4071 ATAACTTAAC

                                *          *
       4081 AACTCAATAACTTAAAAT-ATAACTTTCAAAT
          1 AACTCAATAA-TTAAAATGAAAACTTTCAAAA

              *         *                  
       4112 AATTCAATAATTTAAATGAAAACTTTCAAAA
          1 AACTCAATAATTAAAATGAAAACTTTCAAAA

                      
       4143 AACTCAATAA
          1 AACTCAATAA

       4153 AAATTTTGCA


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  30    6  0.17
  31   29  0.83

ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31


Consensus pattern (31 bp):   
AACTCAATAATTAAAATGAAAACTTTCAAAA
Done.