Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2984

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: 22498
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34


Found at i:599 original size:27 final size:28

Alignment explanation


    Indices: 569--621  Score: 72
    Period size: 27  Copynumber: 1.9  Consensus size: 28

        559 TTAATCACTG

                         *              
        569 TATTTTAAAATTTTAAAATTC-AATCCC
          1 TATTTTAAAATTTAAAAATTCTAATCCC

                  **                  
        596 TATTTTTCAATTTAAAAATTCTAATC
          1 TATTTTAAAATTTAAAAATTCTAATC

        622 TATTTTTCTA


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  27   18  0.82
  28    4  0.18

ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47


Consensus pattern (28 bp):   
TATTTTAAAATTTAAAAATTCTAATCCC

Found at i:628 original size:27 final size:26

Alignment explanation


    Indices: 577--629  Score: 72
    Period size: 27  Copynumber: 2.0  Consensus size: 26

        567 TGTATTTTAA

                 *                     
        577 AATTTTAAAATTCAATCCCTATTTTTC
          1 AATTTAAAAATTCAAT-CCTATTTTTC

                                       
        604 AATTTAAAAATTCTAAT-CTATTTTTC
          1 AATTTAAAAATTC-AATCCTATTTTTC

        630 TATAAGAAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  26    9  0.38
  27   12  0.50
  28    3  0.12

ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49


Consensus pattern (26 bp):   
AATTTAAAAATTCAATCCTATTTTTC

Found at i:5259 original size:14 final size:15

Alignment explanation


    Indices: 5235--5263  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       5225 TGCAGGTTGG

                           
       5235 TTTAGTTTTTATTTA
          1 TTTAGTTTTTATTTA

                           
       5250 TTTA-TTTTTATTTA
          1 TTTAGTTTTTATTTA

       5264 ACTGTAAAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76


Consensus pattern (15 bp):   
TTTAGTTTTTATTTA

Found at i:17691 original size:12 final size:12

Alignment explanation


    Indices: 17674--17698  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      17664 TCGGCAGATC

                        
      17674 AGCAAGTAGAAG
          1 AGCAAGTAGAAG

                        
      17686 AGCAAGTAGAAG
          1 AGCAAGTAGAAG

             
      17698 A
          1 A

      17699 TGAGTTGGCT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.52, C:0.08, G:0.32, T:0.08


Consensus pattern (12 bp):   
AGCAAGTAGAAG
Done.