Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2204

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: 16930
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30


Found at i:2595 original size:28 final size:29

Alignment explanation


    Indices: 2563--2617  Score: 76
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       2553 ACAGGCGACC

                               *         
       2563 ACACGGGAGTGT-CTAGGCTGTGTGAAGG
          1 ACACGGGAGTGTGCTAGGCCGTGTGAAGG

                   *       *           
       2591 ACACGGGCGTGTGCTTGGCCGTGTGAA
          1 ACACGGGAGTGTGCTAGGCCGTGTGAA

       2618 AACCCTTGTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  28   11  0.48
  29   12  0.52

ACGTcount: A:0.18, C:0.18, G:0.42, T:0.22


Consensus pattern (29 bp):   
ACACGGGAGTGTGCTAGGCCGTGTGAAGG

Found at i:4100 original size:36 final size:36

Alignment explanation


    Indices: 4053--4124  Score: 126
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       4043 TCTCCTGAGT

                                     *          
       4053 ACAAAACATGAAATAACCGGATTAAGAGCACCAAAA
          1 ACAAAACATGAAATAACCGGATTAAAAGCACCAAAA

                                        *       
       4089 ACAAAACATGAAATAACCGGATTAAAAGTACCAAAA
          1 ACAAAACATGAAATAACCGGATTAAAAGCACCAAAA

       4125 TCCACAAATC


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  36   34  1.00

ACGTcount: A:0.57, C:0.18, G:0.12, T:0.12


Consensus pattern (36 bp):   
ACAAAACATGAAATAACCGGATTAAAAGCACCAAAA

Found at i:9294 original size:28 final size:29

Alignment explanation


    Indices: 9262--9316  Score: 76
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       9252 ACAGGCGACC

                               *         
       9262 ACACGGGAGTGT-CTAGGCTGTGTGAAGG
          1 ACACGGGAGTGTGCTAGGCCGTGTGAAGG

                   *       *           
       9290 ACACGGGCGTGTGCTTGGCCGTGTGAA
          1 ACACGGGAGTGTGCTAGGCCGTGTGAA

       9317 AACCCTTGTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  28   11  0.48
  29   12  0.52

ACGTcount: A:0.18, C:0.18, G:0.42, T:0.22


Consensus pattern (29 bp):   
ACACGGGAGTGTGCTAGGCCGTGTGAAGG

Found at i:10801 original size:36 final size:36

Alignment explanation


    Indices: 10754--10825  Score: 126
    Period size: 36  Copynumber: 2.0  Consensus size: 36

      10744 TCTCCTGAGT

                                     *          
      10754 ACAAAACATGAAATAACCGGATTAAGAGCACCAAAA
          1 ACAAAACATGAAATAACCGGATTAAAAGCACCAAAA

                                        *       
      10790 ACAAAACATGAAATAACCGGATTAAAAGTACCAAAA
          1 ACAAAACATGAAATAACCGGATTAAAAGCACCAAAA

      10826 TCCACAAATC


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  36   34  1.00

ACGTcount: A:0.57, C:0.18, G:0.12, T:0.12


Consensus pattern (36 bp):   
ACAAAACATGAAATAACCGGATTAAAAGCACCAAAA

Found at i:16302 original size:28 final size:29

Alignment explanation


    Indices: 16270--16324  Score: 76
    Period size: 29  Copynumber: 1.9  Consensus size: 29

      16260 ACAGGCGACC

                               *         
      16270 ACACGGGAGTGT-CTAGGCTGTGTGAAGG
          1 ACACGGGAGTGTGCTAGGCCGTGTGAAGG

                   *       *           
      16298 ACACGGGCGTGTGCTTGGCCGTGTGAA
          1 ACACGGGAGTGTGCTAGGCCGTGTGAA

      16325 AACCCCTGTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  28   11  0.48
  29   12  0.52

ACGTcount: A:0.18, C:0.18, G:0.42, T:0.22


Consensus pattern (29 bp):   
ACACGGGAGTGTGCTAGGCCGTGTGAAGG
Done.