Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1009 ID=scaffold_1009-JGI_221_v2.0

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: 3853
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.15

Warning! 2322 characters in sequence are not A, C, G, or T


Found at i:2482 original size:25 final size:25

Alignment explanation


    Indices: 2448--2502  Score: 110
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       2438 CACATTAATT

                                     
       2448 ATAATTTAAGTAACAATTGATATAC
          1 ATAATTTAAGTAACAATTGATATAC

                                     
       2473 ATAATTTAAGTAACAATTGATATAC
          1 ATAATTTAAGTAACAATTGATATAC

                 
       2498 ATAAT
          1 ATAAT

       2503 ATAGTTGATA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   30  1.00

ACGTcount: A:0.49, C:0.07, G:0.07, T:0.36


Consensus pattern (25 bp):   
ATAATTTAAGTAACAATTGATATAC

Found at i:2512 original size:18 final size:18

Alignment explanation


    Indices: 2489--2527  Score: 69
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       2479 TAAGTAACAA

                      *       
       2489 TTGATATACATAATATAG
          1 TTGATATACAAAATATAG

                              
       2507 TTGATATACAAAATATAG
          1 TTGATATACAAAATATAG

               
       2525 TTG
          1 TTG

       2528 TAAAAAATCA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38


Consensus pattern (18 bp):   
TTGATATACAAAATATAG
Done.