Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2256

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: 14342
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26


Found at i:5339 original size:27 final size:27

Alignment explanation


    Indices: 5301--5353  Score: 106
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       5291 TCACTAACTA

                                       
       5301 ATACTAATCTAATACTAATAGAATAGT
          1 ATACTAATCTAATACTAATAGAATAGT

                                      
       5328 ATACTAATCTAATACTAATAGAATAG
          1 ATACTAATCTAATACTAATAGAATAG

       5354 AAAAAATAGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32


Consensus pattern (27 bp):   
ATACTAATCTAATACTAATAGAATAGT

Found at i:5340 original size:5 final size:6

Alignment explanation


    Indices: 5297--5347  Score: 56
    Period size: 6  Copynumber: 9.2  Consensus size: 6

       5287 GGGATCACTA

                                          *     *                  
       5297 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT AGT-AT ACTAAT -CTAAT
          1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT

                    
       5341 ACTAAT A
          1 ACTAAT A

       5348 GAATAGAAAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 8
        0.78            0.06        0.16

Matches are distributed among these distances:
   5   18  0.47
   6   20  0.53

ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33


Consensus pattern (6 bp):   
ACTAAT

Found at i:5363 original size:14 final size:14

Alignment explanation


    Indices: 5344--5371  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       5334 ATCTAATACT

                          
       5344 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

                          
       5358 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

       5372 TACTAATATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14


Consensus pattern (14 bp):   
AATAGAATAGAAAA
Done.