Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2144

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: 9528
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:1051 original size:2 final size:2

Alignment explanation


    Indices: 1044--1082  Score: 64
    Period size: 2  Copynumber: 20.5  Consensus size: 2

       1034 AGTTTGGGGT

                                                                         
       1044 TA TA TA TA TA T- TA TA TA -A 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 TA TA TA T

       1083 GTATGTCTAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   1    2  0.06
   2   33  0.94

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


Consensus pattern (2 bp):   
TA

Found at i:2906 original size:22 final size:21

Alignment explanation


    Indices: 2880--2928  Score: 62
    Period size: 22  Copynumber: 2.3  Consensus size: 21

       2870 TTATGTTTAA

                          * *    
       2880 AAAAATATATTAAATATAAAT
          1 AAAAATATATTAAAAAAAAAT

                     *            
       2901 ATAAAATATTTTAAAAAAAAAT
          1 A-AAAATATATTAAAAAAAAAT

                  
       2923 AAAAAT
          1 AAAAAT

       2929 TTTGGATAAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  21    6  0.25
  22   18  0.75

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (21 bp):   
AAAAATATATTAAAAAAAAAT

Found at i:5416 original size:9 final size:9

Alignment explanation


    Indices: 5402--5427  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

       5392 ATTAAAATTT

                     
       5402 ATTTATATA
          1 ATTTATATA

                     
       5411 ATTTATATA
          1 ATTTATATA

                    
       5420 ATTTATAT
          1 ATTTATAT

       5428 GAGTAGTATA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (9 bp):   
ATTTATATA

Found at i:5546 original size:12 final size:12

Alignment explanation


    Indices: 5529--5568  Score: 53
    Period size: 12  Copynumber: 3.3  Consensus size: 12

       5519 TTTTGTAATT

                  *     
       5529 TTTTAAAATTAA
          1 TTTTAATATTAA

                   *    
       5541 TTTTAATTTTAA
          1 TTTTAATATTAA

                      * 
       5553 TTTTAATATTTA
          1 TTTTAATATTAA

                
       5565 TTTT
          1 TTTT

       5569 TTTAAAAAAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  12   24  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (12 bp):   
TTTTAATATTAA
Done.