Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold489

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: 192533
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35


File 2 of 2

Found at i:188798 original size:58 final size:57

Alignment explanation


    Indices: 188688--188799  Score: 138
    Period size: 57  Copynumber: 1.9  Consensus size: 57

     188678 TATTTTAGGG

                                **               *                   
     188688 CCATTTAAGTTATTTAACAAGGTCTAGGTCATTTTAATAATTTTCATCATTTTAACA
          1 CCATTTAAGTTATTTAACAAACTCTAGGTCATTTTAACAATTTTCATCATTTTAACA

                   *                             *                   
     188745 CCATTTAGGTTATTTAACAAAACT-TAGAGTCATTTTCACAA-TTTCTATCATTTTA
          1 CCATTTAAGTTATTTAAC-AAACTCTAG-GTCATTTTAACAATTTTC-ATCATTTTA

     188800 GAGTCATGTA


Statistics
Matches: 47,  Mismatches: 5, Indels: 5
        0.82            0.09        0.09

Matches are distributed among these distances:
  57   24  0.51
  58   23  0.49

ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44


Consensus pattern (57 bp):   
CCATTTAAGTTATTTAACAAACTCTAGGTCATTTTAACAATTTTCATCATTTTAACA

Found at i:190295 original size:19 final size:18

Alignment explanation


    Indices: 190267--190302  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

     190257 GATTATTATT

                        *     
     190267 TTAATAAAATTTTTTAAG
          1 TTAATAAAATTTATTAAG

                              
     190285 TTAATTAAAATTTATTAA
          1 TTAA-TAAAATTTATTAA

     190303 AAAGATTTCT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    4  0.25
  19   12  0.75

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (18 bp):   
TTAATAAAATTTATTAAG

Done.