Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00648.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: 4065
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35


Found at i:381 original size:22 final size:22

Alignment explanation


    Indices: 356--398  Score: 77
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        346 ATTAATGTTT

                     *            
        356 TGTTAGCTTTGTGATTATTGCG
          1 TGTTAGCTTCGTGATTATTGCG

                                 
        378 TGTTAGCTTCGTGATTATTGC
          1 TGTTAGCTTCGTGATTATTGC

        399 TTGATCTAGG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.14, C:0.12, G:0.26, T:0.49


Consensus pattern (22 bp):   
TGTTAGCTTCGTGATTATTGCG

Found at i:1590 original size:22 final size:22

Alignment explanation


    Indices: 1562--1605  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1552 ACCTAAGGAA

                                  
       1562 GTCTCTTTAAAAGGTAACTCAT
          1 GTCTCTTTAAAAGGTAACTCAT

                                  
       1584 GTCTCTTTAAAAGGTAACTCAT
          1 GTCTCTTTAAAAGGTAACTCAT

       1606 TTACTCAATC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36


Consensus pattern (22 bp):   
GTCTCTTTAAAAGGTAACTCAT

Found at i:3470 original size:72 final size:72

Alignment explanation


    Indices: 3353--3502  Score: 273
    Period size: 72  Copynumber: 2.1  Consensus size: 72

       3343 TTCAGCATCA

                       *          *                                          
       3353 GTTACTGCTTCTTGCTCCTCCTGCAACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATT
          1 GTTACTGCTTCCTGCTCCTCCTACAACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATT

                   
       3418 AATATTT
         66 AATATTT

                                                                             
       3425 GTTACTGCTTCCTGCTCCTCCTACAACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATT
          1 GTTACTGCTTCCTGCTCCTCCTACAACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATT

                   
       3490 AATATTT
         66 AATATTT

             *    
       3497 GGTACT
          1 GTTACT

       3503 ATCGAGCACC


Statistics
Matches: 75,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  72   75  1.00

ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39


Consensus pattern (72 bp):   
GTTACTGCTTCCTGCTCCTCCTACAACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATT
AATATTT

Found at i:3881 original size:21 final size:21

Alignment explanation


    Indices: 3855--3899  Score: 72
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       3845 ACTTAGAGCA

                        *      * 
       3855 GAGGCAGCAGCGCGGGAGGTG
          1 GAGGCAGCAGCGAGGGAGGAG

                                 
       3876 GAGGCAGCAGCGAGGGAGGAG
          1 GAGGCAGCAGCGAGGGAGGAG

               
       3897 GAG
          1 GAG

       3900 TAGAATAGAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.24, C:0.16, G:0.58, T:0.02


Consensus pattern (21 bp):   
GAGGCAGCAGCGAGGGAGGAG

Done.