Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g00228.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, 472

Length: 787
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30


Found at i:8 original size:3 final size:3

Alignment explanation


    Indices: 1--35  Score: 52
    Period size: 3  Copynumber: 11.7  Consensus size: 3

                        *                       *         
          1 GAA GAA GAA AAA GAA GAA GAA GAA GAA TAA GAA GA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA

         36 GAAAAAATGG


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   3   28  1.00

ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03


Consensus pattern (3 bp):   
GAA

Found at i:15 original size:9 final size:9

Alignment explanation


    Indices: 2--40  Score: 51
    Period size: 9  Copynumber: 4.2  Consensus size: 9

          1 G

                     
          2 AAGAAGAAA
          1 AAGAAGAAA

                    *
         11 AAGAAGAAG
          1 AAGAAGAAA

                    *
         20 AAGAAGAAT
          1 AAGAAGAAA

                      
         29 AAGAAGAGAA
          1 AAGAAGA-AA

              
         39 AA
          1 AA

         41 AATGGAGATG


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
   9   23  0.88
  10    3  0.12

ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03


Consensus pattern (9 bp):   
AAGAAGAAA

Found at i:396 original size:25 final size:25

Alignment explanation


    Indices: 362--409  Score: 78
    Period size: 25  Copynumber: 1.9  Consensus size: 25

        352 GTTGCAATGG

                                     
        362 TTGAGGAGTAAGCCTCTAAAATCAT
          1 TTGAGGAGTAAGCCTCTAAAATCAT

                         * *       
        387 TTGAGGAGTAAGCTTTTAAAATC
          1 TTGAGGAGTAAGCCTCTAAAATC

        410 TCTAAAATCA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  25   21  1.00

ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31


Consensus pattern (25 bp):   
TTGAGGAGTAAGCCTCTAAAATCAT

Found at i:418 original size:34 final size:34

Alignment explanation


    Indices: 375--443  Score: 129
    Period size: 34  Copynumber: 2.0  Consensus size: 34

        365 AGGAGTAAGC

                                       *      
        375 CTCTAAAATCATTTGAGGAGTAAGCTTTTAAAAT
          1 CTCTAAAATCATTTGAGGAGTAAGCTTCTAAAAT

                                              
        409 CTCTAAAATCATTTGAGGAGTAAGCTTCTAAAAT
          1 CTCTAAAATCATTTGAGGAGTAAGCTTCTAAAAT

             
        443 C
          1 C

        444 ATTCTTGATG


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:0.38, C:0.14, G:0.14, T:0.33


Consensus pattern (34 bp):   
CTCTAAAATCATTTGAGGAGTAAGCTTCTAAAAT
Done.