Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1698

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: 4771
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37


Found at i:1043 original size:18 final size:18

Alignment explanation


    Indices: 1020--1054  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

       1010 GAGCATCGGC

                   *          
       1020 TTTTTTTCTTC-TTTCTT
          1 TTTTTTTTTTCGTTTCTT

                              
       1037 TTTTTTTTTTCGTTTCTT
          1 TTTTTTTTTTCGTTTCTT

       1055 GGTCCCACTC


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

Matches are distributed among these distances:
  17   10  0.62
  18    6  0.38

ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83


Consensus pattern (18 bp):   
TTTTTTTTTTCGTTTCTT

Found at i:1550 original size:18 final size:18

Alignment explanation


    Indices: 1523--1558  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       1513 TCTGTGTGCA

                              
       1523 CATTAACACAACTTCCTC
          1 CATTAACACAACTTCCTC

                 *            
       1541 CATTAGCACAACTTCCTC
          1 CATTAACACAACTTCCTC

       1559 GAAACTTGCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.31, C:0.39, G:0.03, T:0.28


Consensus pattern (18 bp):   
CATTAACACAACTTCCTC

Found at i:4145 original size:2 final size:2

Alignment explanation


    Indices: 4138--4172  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       4128 TATTGTATTT

                                                                
       4138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       4173 TTGTACTTAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:4729 original size:12 final size:12

Alignment explanation


    Indices: 4712--4738  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       4702 AATGGCCTAA

                        
       4712 CCACATATCTGG
          1 CCACATATCTGG

                        
       4724 CCACATATCTGG
          1 CCACATATCTGG

               
       4736 CCA
          1 CCA

       4739 GCAGATGAGC


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

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.26, C:0.37, G:0.15, T:0.22


Consensus pattern (12 bp):   
CCACATATCTGG
Done.