Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g00577.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: 4736
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28


Found at i:4319 original size:21 final size:21

Alignment explanation


    Indices: 4294--4348  Score: 58
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       4284 GGATGATGAG

                                * 
       4294 GATGAGGAAGATGAAGCA-GGA
          1 GATGAGGAAGATGAAG-ATGCA

                 **              
       4315 GATGATCAAGATGAAGATGCA
          1 GATGAGGAAGATGAAGATGCA

                    *    
       4336 GATGAGGAGGATG
          1 GATGAGGAAGATG

       4349 CATCTGGTGA


Statistics
Matches: 27,  Mismatches: 6, Indels: 2
        0.77            0.17        0.06

Matches are distributed among these distances:
  20    1  0.04
  21   26  0.96

ACGTcount: A:0.40, C:0.05, G:0.40, T:0.15


Consensus pattern (21 bp):   
GATGAGGAAGATGAAGATGCA

Found at i:4434 original size:15 final size:15

Alignment explanation


    Indices: 4414--4442  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       4404 TGCCAGTGGA

                           
       4414 GACGAGGATGATGAG
          1 GACGAGGATGATGAG

                          
       4429 GACGAGGATGATGA
          1 GACGAGGATGATGA

       4443 CGATGACGAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.34, C:0.07, G:0.45, T:0.14


Consensus pattern (15 bp):   
GACGAGGATGATGAG

Found at i:4479 original size:9 final size:9

Alignment explanation


    Indices: 4468--4514  Score: 58
    Period size: 9  Copynumber: 5.2  Consensus size: 9

       4458 TGATGGTGAG

                    *
       4468 GAAGAGGAG
          1 GAAGAGGAA

                 *   
       4477 GAAGAAGAA
          1 GAAGAGGAA

                     
       4486 GAAGAGGAA
          1 GAAGAGGAA

              *     *
       4495 GACGAGGAT
          1 GAAGAGGAA

                     
       4504 GAAGAGGAA
          1 GAAGAGGAA

              
       4513 GA
          1 GA

       4515 GCTTCAGCCA


Statistics
Matches: 31,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
   9   31  1.00

ACGTcount: A:0.51, C:0.02, G:0.45, T:0.02


Consensus pattern (9 bp):   
GAAGAGGAA

Found at i:4501 original size:24 final size:24

Alignment explanation


    Indices: 4465--4515  Score: 75
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       4455 CGATGATGGT

                    *               
       4465 GAGGAAGAGGAGGAAGAAGAAGAA
          1 GAGGAAGACGAGGAAGAAGAAGAA

                          *     *   
       4489 GAGGAAGACGAGGATGAAGAGGAA
          1 GAGGAAGACGAGGAAGAAGAAGAA

               
       4513 GAG
          1 GAG

       4516 CTTCAGCCAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.49, C:0.02, G:0.47, T:0.02


Consensus pattern (24 bp):   
GAGGAAGACGAGGAAGAAGAAGAA
Done.