Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00652.M2

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: 5561
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34


Found at i:1229 original size:40 final size:40

Alignment explanation


    Indices: 1169--1248  Score: 151
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       1159 GGGAATGTAC

                                                    
       1169 AGAAGTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
          1 AGAAGTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA

                *                                   
       1209 AGAATTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
          1 AGAAGTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA

       1249 TTAACTCTTG


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  40   39  1.00

ACGTcount: A:0.25, C:0.10, G:0.29, T:0.36


Consensus pattern (40 bp):   
AGAAGTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA

Found at i:1258 original size:40 final size:40

Alignment explanation


    Indices: 1169--1258  Score: 144
    Period size: 40  Copynumber: 2.2  Consensus size: 40

       1159 GGGAATGTAC

                *                                   
       1169 AGAAGTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
          1 AGAACTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA

                *                                   
       1209 AGAATTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA
          1 AGAACTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA

            **        
       1249 TTAACTCTTG
          1 AGAACTCTTG

       1259 CTTCCATCGA


Statistics
Matches: 46,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  40   46  1.00

ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38


Consensus pattern (40 bp):   
AGAACTCTTGTTGCGTCATCTTGGTGAAAGGTATGTTGAA

Found at i:3936 original size:34 final size:34

Alignment explanation


    Indices: 3893--3961  Score: 129
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       3883 CGAAGATAAT

                                 *            
       3893 GCCAGTAGAACAGTCCATAGAGAGCTAATGGATG
          1 GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG

                                              
       3927 GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG
          1 GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG

             
       3961 G
          1 G

       3962 TTCATCACCT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   34  1.00

ACGTcount: A:0.36, C:0.17, G:0.29, T:0.17


Consensus pattern (34 bp):   
GCCAGTAGAACAGTCCATAGAAAGCTAATGGATG
Done.