Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1032

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: 3229
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.26

Warning! 566 characters in sequence are not A, C, G, or T


Found at i:2337 original size:9 final size:9

Alignment explanation


    Indices: 2325--2377  Score: 54
    Period size: 9  Copynumber: 5.9  Consensus size: 9

       2315 AAAAATTGAA

                     
       2325 AAAAAAATC
          1 AAAAAAATC

                     
       2334 AAAAAAATC
          1 AAAAAAATC

                   **
       2343 AAAAAAAGA
          1 AAAAAAATC

                     *
       2352 AAAATAAATT
          1 AAAA-AAATC

                    *
       2362 AAAAAAA-G
          1 AAAAAAATC

                    
       2370 AAAAAAAT
          1 AAAAAAAT

       2378 TGTATACGGT


Statistics
Matches: 37,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
   8    7  0.19
   9   23  0.62
  10    7  0.19

ACGTcount: A:0.81, C:0.04, G:0.04, T:0.11


Consensus pattern (9 bp):   
AAAAAAATC

Found at i:2360 original size:19 final size:18

Alignment explanation


    Indices: 2334--2376  Score: 68
    Period size: 19  Copynumber: 2.3  Consensus size: 18

       2324 AAAAAAAATC

                              
       2334 AAAAAAATCAAAAAAAGA
          1 AAAAAAATCAAAAAAAGA

                     *         
       2352 AAAATAAATTAAAAAAAGA
          1 AAAA-AAATCAAAAAAAGA

                  
       2371 AAAAAA
          1 AAAAAA

       2377 TTGTATACGG


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  18    6  0.26
  19   17  0.74

ACGTcount: A:0.84, C:0.02, G:0.05, T:0.09


Consensus pattern (18 bp):   
AAAAAAATCAAAAAAAGA
Done.