Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g00276.M4

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: 3967
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24


Found at i:557 original size:6 final size:6

Alignment explanation


    Indices: 548--597  Score: 64
    Period size: 6  Copynumber: 8.3  Consensus size: 6

        538 GGAGAGGGAG

                                    **           *             *   
        548 CGAGAA CGAGAA CGAGAA CGACTA CGAGAA CGGGAA CGAGAA CGTGAA
          1 CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA CGAGAA

              
        596 CG
          1 CG

        598 TTTGCGCATC


Statistics
Matches: 37,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
   6   37  1.00

ACGTcount: A:0.42, C:0.20, G:0.34, T:0.04


Consensus pattern (6 bp):   
CGAGAA

Found at i:640 original size:18 final size:18

Alignment explanation


    Indices: 617--651  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        607 CTTGGAGCGA

                              
        617 CGGGAGAAGGAAAGAGAG
          1 CGGGAGAAGGAAAGAGAG

                       *     
        635 CGGGAGAAGGAGAGAGA
          1 CGGGAGAAGGAAAGAGA

        652 ACGAGAGCGC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.43, C:0.06, G:0.51, T:0.00


Consensus pattern (18 bp):   
CGGGAGAAGGAAAGAGAG

Found at i:3084 original size:45 final size:45

Alignment explanation


    Indices: 3015--3119  Score: 201
    Period size: 45  Copynumber: 2.3  Consensus size: 45

       3005 ATGATTGTGA

                *                                        
       3015 CCAAGGAAGAAACTACCACAGATCAAGTTGAGGAGCCAAAGATGG
          1 CCAATGAAGAAACTACCACAGATCAAGTTGAGGAGCCAAAGATGG

                                                         
       3060 CCAATGAAGAAACTACCACAGATCAAGTTGAGGAGCCAAAGATGG
          1 CCAATGAAGAAACTACCACAGATCAAGTTGAGGAGCCAAAGATGG

                           
       3105 CCAATGAAGAAACTA
          1 CCAATGAAGAAACTA

       3120 ATGTTGATCA


Statistics
Matches: 59,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   59  1.00

ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12


Consensus pattern (45 bp):   
CCAATGAAGAAACTACCACAGATCAAGTTGAGGAGCCAAAGATGG

Found at i:3129 original size:45 final size:45

Alignment explanation


    Indices: 3015--3147  Score: 185
    Period size: 45  Copynumber: 3.0  Consensus size: 45

       3005 ATGATTGTGA

                *          *                             
       3015 CCAAGGAAGAAACTACCACAGATCAAGTTGAGGAGCCAAAGATGG
          1 CCAATGAAGAAACTAACACAGATCAAGTTGAGGAGCCAAAGATGG

                           *                             
       3060 CCAATGAAGAAACTACCACAGATCAAGTTGAGGAGCCAAAGATGG
          1 CCAATGAAGAAACTAACACAGATCAAGTTGAGGAGCCAAAGATGG

                            ****     *           *     
       3105 CCAATGAAGAAACTAATGTTGATCATGTTGAGGAGCCGAAGAT
          1 CCAATGAAGAAACTAACACAGATCAAGTTGAGGAGCCAAAGAT

       3148 AAAAGATGAA


Statistics
Matches: 80,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  45   80  1.00

ACGTcount: A:0.41, C:0.18, G:0.26, T:0.16


Consensus pattern (45 bp):   
CCAATGAAGAAACTAACACAGATCAAGTTGAGGAGCCAAAGATGG
Done.