Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g02664.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: 5721
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30


Found at i:2244 original size:32 final size:33

Alignment explanation


    Indices: 2203--2268  Score: 116
    Period size: 32  Copynumber: 2.0  Consensus size: 33

       2193 GGGCGAGAAC

                                        *    
       2203 TAATTGGCTTCGGTTAGGT-AAAAAATATGACA
          1 TAATTGGCTTCGGTTAGGTAAAAAAATACGACA

                                             
       2235 TAATTGGCTTCGGTTAGGTAAAAAAATACGACA
          1 TAATTGGCTTCGGTTAGGTAAAAAAATACGACA

             
       2268 T
          1 T

       2269 TCTTTCATAG


Statistics
Matches: 32,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  32   19  0.59
  33   13  0.41

ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30


Consensus pattern (33 bp):   
TAATTGGCTTCGGTTAGGTAAAAAAATACGACA

Found at i:5485 original size:27 final size:27

Alignment explanation


    Indices: 5455--5543  Score: 110
    Period size: 27  Copynumber: 3.3  Consensus size: 27

       5445 TCCAGGCCTG

                                       
       5455 AGTTTCTTTTAGTTTTCTAGTTGATTC
          1 AGTTTCTTTTAGTTTTCTAGTTGATTC

                        *        *   *  *
       5482 AGTTTCTTCTT-CTGTTT-TATTTGGTTA
          1 AGTTTCTT-TTAGT-TTTCTAGTTGATTC

                                       
       5509 AGTTTCTTTTAGTTTTCTAGTTGATTC
          1 AGTTTCTTTTAGTTTTCTAGTTGATTC

                    
       5536 AGTTTCTT
          1 AGTTTCTT

       5544 CTTCTGTTTT


Statistics
Matches: 50,  Mismatches: 8, Indels: 8
        0.76            0.12        0.12

Matches are distributed among these distances:
  26    5  0.10
  27   40  0.80
  28    5  0.10

ACGTcount: A:0.13, C:0.11, G:0.15, T:0.61


Consensus pattern (27 bp):   
AGTTTCTTTTAGTTTTCTAGTTGATTC

Found at i:5537 original size:54 final size:54

Alignment explanation


    Indices: 5455--5562  Score: 207
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       5445 TCCAGGCCTG

                                                            *     
       5455 AGTTTCTTTTAGTTTTCTAGTTGATTCAGTTTCTTCTTCTGTTTTATTTGGTTA
          1 AGTTTCTTTTAGTTTTCTAGTTGATTCAGTTTCTTCTTCTGTTTTATTAGGTTA

                                                                  
       5509 AGTTTCTTTTAGTTTTCTAGTTGATTCAGTTTCTTCTTCTGTTTTATTAGGTTA
          1 AGTTTCTTTTAGTTTTCTAGTTGATTCAGTTTCTTCTTCTGTTTTATTAGGTTA

       5563 TTTTGCTTTA


Statistics
Matches: 53,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  54   53  1.00

ACGTcount: A:0.14, C:0.11, G:0.15, T:0.60


Consensus pattern (54 bp):   
AGTTTCTTTTAGTTTTCTAGTTGATTCAGTTTCTTCTTCTGTTTTATTAGGTTA
Done.