Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g01107.C1

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: 9564
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29


Found at i:649 original size:42 final size:42

Alignment explanation


    Indices: 590--678  Score: 178
    Period size: 42  Copynumber: 2.1  Consensus size: 42

        580 ACAGTCTTCA

                                                      
        590 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
          1 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG

                                                      
        632 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
          1 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG

                 
        674 CCAAG
          1 CCAAG

        679 CCAGGAATGA


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   47  1.00

ACGTcount: A:0.47, C:0.18, G:0.28, T:0.07


Consensus pattern (42 bp):   
CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG

Found at i:660 original size:24 final size:24

Alignment explanation


    Indices: 591--663  Score: 77
    Period size: 24  Copynumber: 3.3  Consensus size: 24

        581 CAGTCTTCAC

                                    
        591 CAAGACAGCTGGAAGGCATAGAGT
          1 CAAGACAGCTGGAAGGCATAGAGT

                      **           *
        615 CAAGACA---AAAAGG-A-A-AGC
          1 CAAGACAGCTGGAAGGCATAGAGT

                                    
        633 CAAGACAGCTGGAAGGCATAGAGT
          1 CAAGACAGCTGGAAGGCATAGAGT

                   
        657 CAAGACA
          1 CAAGACA

        664 AAAAGGAAAG


Statistics
Matches: 37,  Mismatches: 6, Indels: 12
        0.67            0.11        0.22

Matches are distributed among these distances:
  18    9  0.24
  19    1  0.03
  20    1  0.03
  21    8  0.22
  22    1  0.03
  23    1  0.03
  24   16  0.43

ACGTcount: A:0.45, C:0.18, G:0.29, T:0.08


Consensus pattern (24 bp):   
CAAGACAGCTGGAAGGCATAGAGT
Done.