Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00110.F2

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, 959

Length: 1599
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28


Found at i:59 original size:26 final size:26

Alignment explanation


    Indices: 29--166  Score: 159
    Period size: 26  Copynumber: 5.1  Consensus size: 26

         19 AATTAGTTGG

                                      
         29 CTCCATATCAAGCTACTCTTGAAAGT
          1 CTCCATATCAAGCTACTCTTGAAAGT

            *     *            *        *
         55 TTCCATGTCAAGAGCATACGCTTGAAAGG
          1 CTCCATATC-A-AGC-TACTCTTGAAAGT

                                      
         84 CTCCATATCAAGCTACTCTTGAAAGT
          1 CTCCATATCAAGCTACTCTTGAAAGT

                             *     *    *
        110 CTCCATATCAAAAGCCTGCTCTTAAAAGG
          1 CTCCATATC--AAG-CTACTCTTGAAAGT

                                      
        139 CTCCATATCAAGCTACTCTTGAAAGT
          1 CTCCATATCAAGCTACTCTTGAAAGT

              
        165 CT
          1 CT

        167 AGCCTGCTCT


Statistics
Matches: 92,  Mismatches: 14, Indels: 12
        0.78            0.12        0.10

Matches are distributed among these distances:
  26   40  0.43
  27    7  0.08
  28    7  0.08
  29   38  0.41

ACGTcount: A:0.31, C:0.26, G:0.14, T:0.28


Consensus pattern (26 bp):   
CTCCATATCAAGCTACTCTTGAAAGT

Found at i:92 original size:55 final size:55

Alignment explanation


    Indices: 27--166  Score: 217
    Period size: 55  Copynumber: 2.5  Consensus size: 55

         17 ACAATTAGTT

                                        *     *    *           *   
         27 GGCTCCATATCAAGCTACTCTTGAAAGTTTCCATGTCAAGAGCATACGCTTGAAA
          1 GGCTCCATATCAAGCTACTCTTGAAAGTCTCCATATCAAAAGCATACGCTTAAAA

                                                       * * *       
         82 GGCTCCATATCAAGCTACTCTTGAAAGTCTCCATATCAAAAGCCTGCTCTTAAAA
          1 GGCTCCATATCAAGCTACTCTTGAAAGTCTCCATATCAAAAGCATACGCTTAAAA

                                          
        137 GGCTCCATATCAAGCTACTCTTGAAAGTCT
          1 GGCTCCATATCAAGCTACTCTTGAAAGTCT

        167 AGCCTGCTCT


Statistics
Matches: 78,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  55   78  1.00

ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28


Consensus pattern (55 bp):   
GGCTCCATATCAAGCTACTCTTGAAAGTCTCCATATCAAAAGCATACGCTTAAAA

Found at i:191 original size:45 final size:45

Alignment explanation


    Indices: 122--208  Score: 156
    Period size: 45  Copynumber: 1.9  Consensus size: 45

        112 CCATATCAAA

                                                 *       
        122 AGCCTGCTCTTAAAAGGCTCCATATCAAGCTACTCTTGAAAGTCT
          1 AGCCTGCTCTTAAAAGGCTCCATATCAAGCTACTCTTAAAAGTCT

                               *                      
        167 AGCCTGCTCTTAAAAGGCTTCATATCAAGCTACTCTTAAAAG
          1 AGCCTGCTCTTAAAAGGCTCCATATCAAGCTACTCTTAAAAG

        209 GATCTCGGGG


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  45   40  1.00

ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29


Consensus pattern (45 bp):   
AGCCTGCTCTTAAAAGGCTCCATATCAAGCTACTCTTAAAAGTCT
Done.