Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g01538.N1

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: 2893
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:155 original size:21 final size:22

Alignment explanation


    Indices: 130--181  Score: 97
    Period size: 22  Copynumber: 2.4  Consensus size: 22

        120 TGAATGATAA

                                  
        130 TGAAATGTTGAA-TAAGTGAAT
          1 TGAAATGTTGAATTAAGTGAAT

                                  
        151 TGAAATGTTGAATTAAGTGAAT
          1 TGAAATGTTGAATTAAGTGAAT

                     
        173 TGAAATGTT
          1 TGAAATGTT

        182 ATATGATTGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  21   12  0.40
  22   18  0.60

ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37


Consensus pattern (22 bp):   
TGAAATGTTGAATTAAGTGAAT

Found at i:2079 original size:45 final size:45

Alignment explanation


    Indices: 2015--2149  Score: 252
    Period size: 45  Copynumber: 3.0  Consensus size: 45

       2005 TTGATCTGTC

                                                         
       2015 AATTCATATACGGGGGTGCCCATTAGGGCACATAACCGGGAAGCA
          1 AATTCATATACGGGGGTGCCCATTAGGGCACATAACCGGGAAGCA

                                                         
       2060 AATTCATATACGGGGGTGCCCATTAGGGCACATAACCGGGAAGCA
          1 AATTCATATACGGGGGTGCCCATTAGGGCACATAACCGGGAAGCA

                                    *           *        
       2105 AATTCATATACGGGGGTGCCCATTGGGGCACATAACTGGGAAGCA
          1 AATTCATATACGGGGGTGCCCATTAGGGCACATAACCGGGAAGCA

       2150 TACTCTCGAG


Statistics
Matches: 88,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   88  1.00

ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19


Consensus pattern (45 bp):   
AATTCATATACGGGGGTGCCCATTAGGGCACATAACCGGGAAGCA

Found at i:2316 original size:23 final size:24

Alignment explanation


    Indices: 2241--2332  Score: 100
    Period size: 24  Copynumber: 3.9  Consensus size: 24

       2231 GGTATATAAT

                       *             
       2241 GGGAAGCTTA-TAAGAGCCATAATC
          1 GGGAAGCTTACAAAGAGCCAT-ATC

                             *       
       2265 GGGAAG-TTCACAAAGAACCATATC
          1 GGGAAGCTT-ACAAAGAGCCATATC

                      **            
       2289 GGGAAGCTTATGAAGAGCC-TATC
          1 GGGAAGCTTACAAAGAGCCATATC

            *                    
       2312 AGGAAGCTTACAAAGAGCCAT
          1 GGGAAGCTTACAAAGAGCCAT

       2333 GTAATGGGAA


Statistics
Matches: 56,  Mismatches: 8, Indels: 8
        0.78            0.11        0.11

Matches are distributed among these distances:
  23   22  0.39
  24   24  0.43
  25   10  0.18

ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18


Consensus pattern (24 bp):   
GGGAAGCTTACAAAGAGCCATATC

Found at i:2326 original size:47 final size:48

Alignment explanation


    Indices: 2241--2332  Score: 127
    Period size: 47  Copynumber: 1.9  Consensus size: 48

       2231 GGTATATAAT

                                    *                       
       2241 GGGAAGCTTATAAGAGCCATAATCGGGAAGTTCACAAAGAACCATATC
          1 GGGAAGCTTATAAGAGCCATAATCAGGAAGTTCACAAAGAACCATATC

                                                      *    
       2289 GGGAAGCTTATGAAGAGCC-T-ATCAGGAAGCTT-ACAAAGAGCCAT
          1 GGGAAGCTTAT-AAGAGCCATAATCAGGAAG-TTCACAAAGAACCAT

       2333 GTAATGGGAA


Statistics
Matches: 40,  Mismatches: 2, Indels: 5
        0.85            0.04        0.11

Matches are distributed among these distances:
  47   19  0.47
  48   14  0.35
  49    7  0.17

ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18


Consensus pattern (48 bp):   
GGGAAGCTTATAAGAGCCATAATCAGGAAGTTCACAAAGAACCATATC
Done.