Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00008.P1

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: 4099
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33


Found at i:1763 original size:20 final size:22

Alignment explanation


    Indices: 1723--1767  Score: 67
    Period size: 20  Copynumber: 2.1  Consensus size: 22

       1713 AGGGATATTT

                                  
       1723 AGGTTTGGGGCCTAAGGGTTTG
          1 AGGTTTGGGGCCTAAGGGTTTG

                          *       
       1745 AGGTTTGGGG-CT-TGGGTTTG
          1 AGGTTTGGGGCCTAAGGGTTTG

               
       1765 AGG
          1 AGG

       1768 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:1917 original size:105 final size:105

Alignment explanation


    Indices: 1735--1945  Score: 332
    Period size: 105  Copynumber: 2.0  Consensus size: 105

       1725 GTTTGGGGCC

                       * *                                      *    *      *
       1735 TAAGGGTTTGAGGTTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGTTGGTGTTTTTGG
          1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA

                  *            *                    
       1800 GCTTTCTTTTAAGTGTTTGTGGCTGTGGACTTCTTAGGTT
         66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT

                                          *        *                         
       1840 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGTGGCTTAAGTTTTACGGTTGGGCTGGTATTTTTGA
          1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA

                                         *          
       1905 GCTTTCGTTTAAGTGTTTGGGGCTGTGGATTTCTTAGGTT
         66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT

             
       1945 T
          1 T

       1946 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:3521 original size:66 final size:66

Alignment explanation


    Indices: 3439--3573  Score: 225
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       3429 AAGTATTGAT

                                                                       *  *  
       3439 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACGCCTAC
          1 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC

             
       3504 C
         66 C

                                     *    *              *                   
       3505 AGGCACTAGATTTGAAGCCAAACTATGTGCGTGCTTGGGCAAACATGGGTATCAGTTACACCAAC
          1 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC

             
       3570 C
         66 C

               
       3571 AGG
          1 AGG

       3574 GTATGTATGA


Statistics
Matches: 64,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  66   64  1.00

ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21


Consensus pattern (66 bp):   
AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC
C
Done.