Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3827

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: 15599
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27


Found at i:8513 original size:18 final size:18

Alignment explanation


    Indices: 8490--8526  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       8480 GCCACTTGGC

                              
       8490 TTCAATGTTCAAAGCAAG
          1 TTCAATGTTCAAAGCAAG

                              
       8508 TTCAATGTTCAAAGCAAG
          1 TTCAATGTTCAAAGCAAG

             
       8526 T
          1 T

       8527 AGAGAAGCAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30


Consensus pattern (18 bp):   
TTCAATGTTCAAAGCAAG

Found at i:13686 original size:17 final size:17

Alignment explanation


    Indices: 13664--13701  Score: 58
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      13654 ACTATCCTTT

                     *     * 
      13664 TTTTTTTTTGTTTTTTA
          1 TTTTTTTTTATTTTTCA

                             
      13681 TTTTTTTTTATTTTTCA
          1 TTTTTTTTTATTTTTCA

                
      13698 TTTT
          1 TTTT

      13702 GGTGCTAAGT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.08, C:0.03, G:0.03, T:0.87


Consensus pattern (17 bp):   
TTTTTTTTTATTTTTCA

Found at i:13690 original size:10 final size:10

Alignment explanation


    Indices: 13661--13695  Score: 54
    Period size: 10  Copynumber: 3.5  Consensus size: 10

      13651 ACTACTATCC

                      
      13661 TTTTTTTTT-
          1 TTTTTTTTTA

                       
      13670 TTTGTTTTTTA
          1 TTT-TTTTTTA

                      
      13681 TTTTTTTTTA
          1 TTTTTTTTTA

                 
      13691 TTTTT
          1 TTTTT

      13696 CATTTTGGTG


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
   9    3  0.12
  10   18  0.75
  11    3  0.12

ACGTcount: A:0.06, C:0.00, G:0.03, T:0.91


Consensus pattern (10 bp):   
TTTTTTTTTA
Done.