Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01334.P2

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: 3512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:2127 original size:3 final size:3

Alignment explanation


    Indices: 2119--2146  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       2109 GAAGTTGCAA

                                                 
       2119 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A

       2147 TTATTATTAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
AAT

Found at i:2376 original size:18 final size:18

Alignment explanation


    Indices: 2355--2404  Score: 50
    Period size: 18  Copynumber: 2.8  Consensus size: 18

       2345 ATTTTACTGT

                            * 
       2355 TTTTTATTAATTTATATA
          1 TTTTTATTAATTTATAAA

                   *      *    
       2373 TTTTTA-AAGATTTTTAAA
          1 TTTTTATTA-ATTTATAAA

                           
       2391 TTTTT-TTAATTTAT
          1 TTTTTATTAATTTAT

       2405 GCTCGTCACA


Statistics
Matches: 25,  Mismatches: 5, Indels: 5
        0.71            0.14        0.14

Matches are distributed among these distances:
  17    6  0.24
  18   19  0.76

ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66


Consensus pattern (18 bp):   
TTTTTATTAATTTATAAA

Found at i:2864 original size:2 final size:2

Alignment explanation


    Indices: 2854--2891  Score: 67
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       2844 TTTTCTTGAA

                                                                    
       2854 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2892 AATTCATTAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   33  0.94
   3    2  0.06

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:2947 original size:2 final size:2

Alignment explanation


    Indices: 2940--2967  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       2930 ACTTTCTAAG

                                                     
       2940 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2968 CATTATAAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.