Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00884.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, 1000

Length: 2048
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27


Found at i:666 original size:12 final size:12

Alignment explanation


    Indices: 651--732  Score: 103
    Period size: 12  Copynumber: 6.8  Consensus size: 12

        641 TAGATGGAAG

                     *  
        651 TGATGATGATTT
          1 TGATGATGAGTT

                        
        663 TGATGATGAGTT
          1 TGATGATGAGTT

            *        *  
        675 CGATGATGAATT
          1 TGATGATGAGTT

                        
        687 TGATGATGAGTT
          1 TGATGATGAGTT

                        *
        699 TGATGATGA-TGA
          1 TGATGATGAGT-T

            *           
        711 AGATGATGAGTT
          1 TGATGATGAGTT

                      
        723 TGATGATGAG
          1 TGATGATGAG

        733 GAATTTGGTC


Statistics
Matches: 59,  Mismatches: 9, Indels: 4
        0.82            0.12        0.06

Matches are distributed among these distances:
  11    1  0.02
  12   57  0.97
  13    1  0.02

ACGTcount: A:0.29, C:0.01, G:0.32, T:0.38


Consensus pattern (12 bp):   
TGATGATGAGTT

Found at i:679 original size:24 final size:24

Alignment explanation


    Indices: 651--731  Score: 117
    Period size: 24  Copynumber: 3.4  Consensus size: 24

        641 TAGATGGAAG

                                    
        651 TGATGATGATTTTGATGATGAGTT
          1 TGATGATGATTTTGATGATGAGTT

            *        *              
        675 CGATGATGAATTTGATGATGAGTT
          1 TGATGATGATTTTGATGATGAGTT

                      ***           
        699 TGATGATGATGAAGATGATGAGTT
          1 TGATGATGATTTTGATGATGAGTT

                     
        723 TGATGATGA
          1 TGATGATGA

        732 GGAATTTGGT


Statistics
Matches: 50,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   50  1.00

ACGTcount: A:0.30, C:0.01, G:0.31, T:0.38


Consensus pattern (24 bp):   
TGATGATGATTTTGATGATGAGTT

Found at i:1413 original size:30 final size:30

Alignment explanation


    Indices: 1348--1413  Score: 107
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       1338 CGGTAAGAAT

                 *                        
       1348 ATGGGGCAGATGGGCCAAATGGGTGGTCAG
          1 ATGGGTCAGATGGGCCAAATGGGTGGTCAG

                                           
       1378 ATGGGTCAGATGGGTCC-AATGGGTGGTCAG
          1 ATGGGTCAGATGGG-CCAAATGGGTGGTCAG

                  
       1408 ATGGGT
          1 ATGGGT

       1414 TATAACATGG


Statistics
Matches: 34,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  30   32  0.94
  31    2  0.06

ACGTcount: A:0.21, C:0.12, G:0.45, T:0.21


Consensus pattern (30 bp):   
ATGGGTCAGATGGGCCAAATGGGTGGTCAG
Done.