Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1216

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: 10254
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37


Found at i:8207 original size:2 final size:2

Alignment explanation


    Indices: 8195--8226  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       8185 GGCTCTTTAT

                                                             
       8195 TA TA T- 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 T

       8227 CATGTAGATA


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:8397 original size:2 final size:2

Alignment explanation


    Indices: 8392--8431  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       8382 ATTTTTTGGT

                                                                       
       8392 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       8432 GTGTTTTAGT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:8914 original size:15 final size:15

Alignment explanation


    Indices: 8894--8924  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       8884 AACAATGAGT

                     *     
       8894 GGTGGTGGTGGTGGA
          1 GGTGGTGGTAGTGGA

                           
       8909 GGTGGTGGTAGTGGA
          1 GGTGGTGGTAGTGGA

             
       8924 G
          1 G

       8925 AACTGGAGGG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.10, C:0.00, G:0.65, T:0.26


Consensus pattern (15 bp):   
GGTGGTGGTAGTGGA
Done.