Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g00725.F2

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: 3203
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32


Found at i:204 original size:11 final size:11

Alignment explanation


    Indices: 188--213  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

        178 GTGTTAGGGC

                       
        188 TTTTTTTTTCT
          1 TTTTTTTTTCT

                       
        199 TTTTTTTTTCT
          1 TTTTTTTTTCT

                
        210 TTTT
          1 TTTT

        214 CTCTTTCCCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92


Consensus pattern (11 bp):   
TTTTTTTTTCT

Found at i:287 original size:25 final size:25

Alignment explanation


    Indices: 248--307  Score: 68
    Period size: 24  Copynumber: 2.4  Consensus size: 25

        238 CGCCTTCTCA

                                      
        248 AAAAGAAAAAAAAAAAGAAGAAAA-G
          1 AAAAG-AAAAAAAAAAGAAGAAAAGG

                    * *       *      
        273 AAAAGAAAGATAAAAGAATAAAAGG
          1 AAAAGAAAAAAAAAAGAAGAAAAGG

               *      
        298 AAATGAAAAA
          1 AAAAGAAAAA

        308 TTTCTCTCGT


Statistics
Matches: 29,  Mismatches: 5, Indels: 2
        0.81            0.14        0.06

Matches are distributed among these distances:
  24   15  0.52
  25   14  0.48

ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05


Consensus pattern (25 bp):   
AAAAGAAAAAAAAAAGAAGAAAAGG

Found at i:2144 original size:16 final size:16

Alignment explanation


    Indices: 2123--2153  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       2113 TCTCTCTATA

                    *       
       2123 TATATATGTATGTATG
          1 TATATATGAATGTATG

                           
       2139 TATATATGAATGTAT
          1 TATATATGAATGTAT

       2154 ATATTCAGTT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48


Consensus pattern (16 bp):   
TATATATGAATGTATG
Done.