Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03994.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: 2370
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.20


Found at i:539 original size:24 final size:25

Alignment explanation


    Indices: 486--544  Score: 70
    Period size: 24  Copynumber: 2.4  Consensus size: 25

        476 TGGATGAGAT

                        *            
        486 GAAAGAAGAA-GATGAAGAAGAGCA
          1 GAAAGAAGAAGGCTGAAGAAGAGCA

             *                        
        510 GGAAG-AGAAGGCTGAAGAAGAGTC-
          1 GAAAGAAGAAGGCTGAAGAAGAG-CA

                       
        534 GAAAGAAGAAG
          1 GAAAGAAGAAG

        545 AAGATGAGGA


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  23    4  0.14
  24   19  0.66
  25    6  0.21

ACGTcount: A:0.53, C:0.05, G:0.37, T:0.05


Consensus pattern (25 bp):   
GAAAGAAGAAGGCTGAAGAAGAGCA

Found at i:609 original size:21 final size:21

Alignment explanation


    Indices: 560--609  Score: 82
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        550 GAGGAGGAGC

                   *             
        560 ATGAAGAAAAGGATGGAGATG
          1 ATGAAGAGAAGGATGGAGATG

                            *    
        581 ATGAAGAGAAGGATGGGGATG
          1 ATGAAGAGAAGGATGGAGATG

                    
        602 ATGAAGAG
          1 ATGAAGAG

        610 GAGCAAGAAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.44, C:0.00, G:0.42, T:0.14


Consensus pattern (21 bp):   
ATGAAGAGAAGGATGGAGATG

Found at i:1350 original size:3 final size:3

Alignment explanation


    Indices: 1342--1412  Score: 58
    Period size: 3  Copynumber: 23.7  Consensus size: 3

       1332 GGATGAGTCT

                              *   *                                     
       1342 GAA GAA GAA GAA GAG GAG GAA GAA GAA GAA -AA GGAA GAA GAA G-A
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA

                       *      *                 
       1386 GAA GGAA GAG GAA -CA GAA TGAA GAA GA
          1 GAA -GAA GAA GAA GAA GAA -GAA GAA GA

       1413 GAAAAATGAA


Statistics
Matches: 56,  Mismatches: 6, Indels: 12
        0.76            0.08        0.16

Matches are distributed among these distances:
   2    5  0.09
   3   43  0.77
   4    8  0.14

ACGTcount: A:0.59, C:0.01, G:0.38, T:0.01


Consensus pattern (3 bp):   
GAA

Found at i:1365 original size:15 final size:15

Alignment explanation


    Indices: 1345--1412  Score: 91
    Period size: 15  Copynumber: 4.5  Consensus size: 15

       1335 TGAGTCTGAA

                        *  
       1345 GAAGAAGAAGAGGAG
          1 GAAGAAGAAGAGAAG

                       *   
       1360 GAAGAAGAAGAAAAG
          1 GAAGAAGAAGAGAAG

                           
       1375 GAAGAAGAAGAGAAG
          1 GAAGAAGAAGAGAAG

                 *   *    *
       1390 GAAGAGGAACAGAAT
          1 GAAGAAGAAGAGAAG

                    
       1405 GAAGAAGA
          1 GAAGAAGA

       1413 GAAAAATGAA


Statistics
Matches: 46,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  15   46  1.00

ACGTcount: A:0.59, C:0.01, G:0.38, T:0.01


Consensus pattern (15 bp):   
GAAGAAGAAGAGAAG

Found at i:1393 original size:27 final size:25

Alignment explanation


    Indices: 1346--1415  Score: 77
    Period size: 27  Copynumber: 2.6  Consensus size: 25

       1336 GAGTCTGAAG

                      *               
       1346 AAGAAGAAGAGGAGGAAGAAGAAGAA
          1 AAGAAGAAGAAGA-GAAGAAGAAGAA

                                   *   
       1372 AAGGAAGAAGAAGAGAAGGAAGAGGAA
          1 AA-GAAGAAGAAGAGAA-GAAGAAGAA

            *                
       1399 CAGAATGAAGAAGAGAA
          1 AAGAA-GAAGAAGAGAA

       1416 AAATGAAAAT


Statistics
Matches: 38,  Mismatches: 3, Indels: 5
        0.83            0.07        0.11

Matches are distributed among these distances:
  26    8  0.21
  27   30  0.79

ACGTcount: A:0.60, C:0.01, G:0.37, T:0.01


Consensus pattern (25 bp):   
AAGAAGAAGAAGAGAAGAAGAAGAA
Done.