Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3325

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: 26799
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:312 original size:20 final size:20

Alignment explanation


    Indices: 287--325  Score: 78
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        277 TTCAGATATT

                                
        287 ATACACTTCCGTTGATCTAG
          1 ATACACTTCCGTTGATCTAG

                               
        307 ATACACTTCCGTTGATCTA
          1 ATACACTTCCGTTGATCTA

        326 AAGTTTAGAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36


Consensus pattern (20 bp):   
ATACACTTCCGTTGATCTAG

Found at i:3556 original size:22 final size:22

Alignment explanation


    Indices: 3526--3567  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       3516 GGAGTTGAAT

                *         *       
       3526 TAAATTATAATTTTTAAGATAG
          1 TAAAATATAATTTTAAAGATAG

                                
       3548 TAAAATATAATTTTAAAGAT
          1 TAAAATATAATTTTAAAGAT

       3568 TAAATCAAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43


Consensus pattern (22 bp):   
TAAAATATAATTTTAAAGATAG

Found at i:4009 original size:3 final size:3

Alignment explanation


    Indices: 4001--4043  Score: 77
    Period size: 3  Copynumber: 14.3  Consensus size: 3

       3991 AAAAACACAT

                                                             *       
       4001 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A

       4044 AAGTATAGAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   3   38  1.00

ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30


Consensus pattern (3 bp):   
ATA

Done.