Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00008.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: 4428
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32


Found at i:2475 original size:20 final size:22

Alignment explanation


    Indices: 2435--2479  Score: 67
    Period size: 20  Copynumber: 2.1  Consensus size: 22

       2425 AGGGATATTT

                                  
       2435 AGGTTTGGGGCCTAAGGGTTTG
          1 AGGTTTGGGGCCTAAGGGTTTG

                          *       
       2457 AGGTTTGGGG-CT-TGGGTTTG
          1 AGGTTTGGGGCCTAAGGGTTTG

               
       2477 AGG
          1 AGG

       2480 CTTAAGGTTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20   10  0.45
  21    2  0.09
  22   10  0.45

ACGTcount: A:0.11, C:0.07, G:0.49, T:0.33


Consensus pattern (22 bp):   
AGGTTTGGGGCCTAAGGGTTTG

Found at i:2629 original size:105 final size:105

Alignment explanation


    Indices: 2447--2657  Score: 332
    Period size: 105  Copynumber: 2.0  Consensus size: 105

       2437 GTTTGGGGCC

                       * *                                      *    *      *
       2447 TAAGGGTTTGAGGTTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGTTGGTGTTTTTGG
          1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA

                  *            *                    
       2512 GCTTTCTTTTAAGTGTTTGTGGCTGTGGACTTCTTAGGTT
         66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT

                                          *        *                         
       2552 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGTGGCTTAAGTTTTACGGTTGGGCTGGTATTTTTGA
          1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA

                                         *          
       2617 GCTTTCGTTTAAGTGTTTGGGGCTGTGGATTTCTTAGGTT
         66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT

             
       2657 T
          1 T

       2658 TGGTTACTGG


Statistics
Matches: 96,  Mismatches: 10, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
 105   96  1.00

ACGTcount: A:0.11, C:0.08, G:0.36, T:0.45


Consensus pattern (105 bp):   
TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA
GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT

Found at i:3847 original size:66 final size:66

Alignment explanation


    Indices: 3770--3902  Score: 221
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       3760 TGGCCTAAGC

                                                                     *  *    
       3770 GCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACGCCTACCA
          1 GCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAACCA

             
       3835 G
         66 G

                                   *    *              *                     
       3836 GCACTAGATTTGAAGCCAAACTATGTGCGTGCTTGGGCAAACATGGGTATCAGTTACACCAACCA
          1 GCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAACCA

             
       3901 G
         66 G

             
       3902 G
          1 G

       3903 GTATGTATGA


Statistics
Matches: 62,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  66   62  1.00

ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22


Consensus pattern (66 bp):   
GCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAACCA
G
Done.