Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1028

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: 19018
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33


Found at i:4324 original size:20 final size:20

Alignment explanation


    Indices: 4299--4353  Score: 74
    Period size: 20  Copynumber: 2.8  Consensus size: 20

       4289 TGTGGTTCAA

                             *  
       4299 CTCATTCGAGCTCAAGTTAG
          1 CTCATTCGAGCTCAAGTCAG

                    *           
       4319 CTCATTCGTGCTCAAGTCAG
          1 CTCATTCGAGCTCAAGTCAG

            *      *       
       4339 GTCATTCAAGCTCAA
          1 CTCATTCGAGCTCAA

       4354 TTTAACTTGT


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   30  1.00

ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29


Consensus pattern (20 bp):   
CTCATTCGAGCTCAAGTCAG

Found at i:12359 original size:10 final size:10

Alignment explanation


    Indices: 12344--12372  Score: 51
    Period size: 9  Copynumber: 3.0  Consensus size: 10

      12334 CGGTATACAA

                      
      12344 ATTTTTTTTT
          1 ATTTTTTTTT

                      
      12354 A-TTTTTTTT
          1 ATTTTTTTTT

                      
      12363 ATTTTTTTTT
          1 ATTTTTTTTT

      12373 CTGAACCTAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
   9    9  0.50
  10    9  0.50

ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90


Consensus pattern (10 bp):   
ATTTTTTTTT

Found at i:12360 original size:9 final size:9

Alignment explanation


    Indices: 12346--12371  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

      12336 GTATACAAAT

                     
      12346 TTTTTTTTA
          1 TTTTTTTTA

                     
      12355 TTTTTTTTA
          1 TTTTTTTTA

                    
      12364 TTTTTTTT
          1 TTTTTTTT

      12372 TCTGAACCTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

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


Consensus pattern (9 bp):   
TTTTTTTTA
Done.