Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold7117.1

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: 8159
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32


Found at i:912 original size:14 final size:14

Alignment explanation


    Indices: 893--920  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

        883 TTTGAATACA

                          
        893 TTAAGTAAGTTAAG
          1 TTAAGTAAGTTAAG

                          
        907 TTAAGTAAGTTAAG
          1 TTAAGTAAGTTAAG

        921 AAATTCTGGT


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:0.43, C:0.00, G:0.21, T:0.36


Consensus pattern (14 bp):   
TTAAGTAAGTTAAG

Found at i:2515 original size:1 final size:1

Alignment explanation


    Indices: 2509--2553  Score: 90
    Period size: 1  Copynumber: 45.0  Consensus size: 1

       2499 CGCATTTATG

                                                         
       2509 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       2554 GGCAGGGTCC


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   44  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:4834 original size:20 final size:20

Alignment explanation


    Indices: 4809--4856  Score: 87
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       4799 CCGTATAATC

                               *
       4809 TTCCGGATCTACAGGCGAAG
          1 TTCCGGATCTACAGGCGAAA

                                
       4829 TTCCGGATCTACAGGCGAAA
          1 TTCCGGATCTACAGGCGAAA

                    
       4849 TTCCGGAT
          1 TTCCGGAT

       4857 TTCGGCCGGT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  20   27  1.00

ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23


Consensus pattern (20 bp):   
TTCCGGATCTACAGGCGAAA
Done.