Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01985.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: 1727
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25


Found at i:62 original size:5 final size:5

Alignment explanation


    Indices: 52--79  Score: 56
    Period size: 5  Copynumber: 5.6  Consensus size: 5

         42 ATTGTGATTC

                                             
         52 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
          1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT

         80 AACGATGAAC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   23  1.00

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (5 bp):   
TTTCT

Found at i:880 original size:48 final size:47

Alignment explanation


    Indices: 827--922  Score: 183
    Period size: 48  Copynumber: 2.0  Consensus size: 47

        817 AAAGGAGTTC

                                                            
        827 AGAAGTAGCCTCTGAGAAAGGAACGCGCAAGGAATTTTCAGTGGTAAG
          1 AGAAGTAGCCTCTGAGAAAGGAACGCGCAAGGAATTTTCAGTGG-AAG

                                                           
        875 AGAAGTAGCCTCTGAGAAAGGAACGCGCAAGGAATTTTCAGTGGAAG
          1 AGAAGTAGCCTCTGAGAAAGGAACGCGCAAGGAATTTTCAGTGGAAG

             
        922 A
          1 A

        923 AAAAGAAAAA


Statistics
Matches: 48,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  47    4  0.08
  48   44  0.92

ACGTcount: A:0.36, C:0.15, G:0.31, T:0.18


Consensus pattern (47 bp):   
AGAAGTAGCCTCTGAGAAAGGAACGCGCAAGGAATTTTCAGTGGAAG

Found at i:939 original size:48 final size:48

Alignment explanation


    Indices: 836--941  Score: 144
    Period size: 48  Copynumber: 2.2  Consensus size: 48

        826 CAGAAGTAGC

                                                    *   * **
        836 CTCTGAGAAAGGAACGCGCAAGGAATTTTCAGTGGTAAGAGAAGTAGC
          1 CTCTGAGAAAGGAACGCGCAAGGAATTTTCAGTGGTAAGAAAAGAAAA

                                                              
        884 CTCTGAGAAAGGAACGCGCAAGGAATTTTCAGTGG-AAGAAAAAGAAAAA
          1 CTCTGAGAAAGGAACGCGCAAGGAATTTTCAGTGGTAAG-AAAAG-AAAA

                      
        933 CT-TGAGAAA
          1 CTCTGAGAAA

        942 CAGCTACATG


Statistics
Matches: 52,  Mismatches: 4, Indels: 4
        0.87            0.07        0.07

Matches are distributed among these distances:
  47    3  0.06
  48   46  0.88
  49    3  0.06

ACGTcount: A:0.42, C:0.13, G:0.28, T:0.17


Consensus pattern (48 bp):   
CTCTGAGAAAGGAACGCGCAAGGAATTTTCAGTGGTAAGAAAAGAAAA
Done.