Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold518

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: 19889
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Found at i:5016 original size:13 final size:13

Alignment explanation


    Indices: 4998--5022  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       4988 ATTACTCAAA

                         
       4998 TGTATCGATACAT
          1 TGTATCGATACAT

                        
       5011 TGTATCGATACA
          1 TGTATCGATACA

       5023 CTGATCTTTG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:13246 original size:14 final size:14

Alignment explanation


    Indices: 13227--13254  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      13217 ATGGCAATTG

                          
      13227 TAAAAAAAAAAAAA
          1 TAAAAAAAAAAAAA

                          
      13241 TAAAAAAAAAAAAA
          1 TAAAAAAAAAAAAA

      13255 AGTGAAGATT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07


Consensus pattern (14 bp):   
TAAAAAAAAAAAAA

Found at i:13247 original size:13 final size:13

Alignment explanation


    Indices: 13229--13253  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      13219 GGCAATTGTA

                         
      13229 AAAAAAAAAAAAT
          1 AAAAAAAAAAAAT

                        
      13242 AAAAAAAAAAAA
          1 AAAAAAAAAAAA

      13254 AAGTGAAGAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.96, C:0.00, G:0.00, T:0.04


Consensus pattern (13 bp):   
AAAAAAAAAAAAT

Found at i:15215 original size:24 final size:24

Alignment explanation


    Indices: 15169--15218  Score: 64
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      15159 TTTGGTAAGA

                              *     
      15169 TTGATTTTCATTTAACTTGATAAT
          1 TTGATTTTCATTTAACTTAATAAT

                    *    * *        
      15193 TTGATTTTTATTTTATTTAATAAT
          1 TTGATTTTCATTTAACTTAATAAT

              
      15217 TT
          1 TT

      15219 TGCTTTTATT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62


Consensus pattern (24 bp):   
TTGATTTTCATTTAACTTAATAAT

Found at i:16271 original size:15 final size:15

Alignment explanation


    Indices: 16251--16280  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      16241 TGACATAAAA

                           
      16251 AAATTATTTTTCAGT
          1 AAATTATTTTTCAGT

                           
      16266 AAATTATTTTTCAGT
          1 AAATTATTTTTCAGT

      16281 TGCTCTATTT


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

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53


Consensus pattern (15 bp):   
AAATTATTTTTCAGT

Found at i:18563 original size:23 final size:23

Alignment explanation


    Indices: 18520--18564  Score: 56
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      18510 GCATATTTTT

                        *          
      18520 ATTTATTATTAATTATATTTAAC
          1 ATTTATTATTAAGTATATTTAAC

                             *     
      18543 ATTTATT-TTACAGTATGTTTAA
          1 ATTTATTATTA-AGTATATTTAA

      18565 ATATAAAAAC


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  22    3  0.16
  23   16  0.84

ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56


Consensus pattern (23 bp):   
ATTTATTATTAAGTATATTTAAC
Done.