Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_544 ID=scaffold_544-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: 5887
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38


Found at i:951 original size:3 final size:3

Alignment explanation


    Indices: 943--996  Score: 72
    Period size: 3  Copynumber: 17.3  Consensus size: 3

        933 TAATTTTTTA

                                               *             *           
        943 ATT ATT ATT ATT ATTT ATT ATT ATT ATA ATT ATT ATT TTCT ATT ATT
          1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT

                     
        990 ATT ATT A
          1 ATT ATT A

        997 GTGTAAGTAC


Statistics
Matches: 45,  Mismatches: 4, Indels: 4
        0.85            0.08        0.08

Matches are distributed among these distances:
   3   40  0.89
   4    5  0.11

ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65


Consensus pattern (3 bp):   
ATT

Found at i:974 original size:22 final size:22

Alignment explanation


    Indices: 943--996  Score: 83
    Period size: 22  Copynumber: 2.5  Consensus size: 22

        933 TAATTTTTTA

                                   
        943 ATTATTATTATTATTTAT-TATT
          1 ATTATTATTATTATTT-TCTATT

                 *                
        965 ATTATAATTATTATTTTCTATT
          1 ATTATTATTATTATTTTCTATT

                      
        987 ATTATTATTA
          1 ATTATTATTA

        997 GTGTAAGTAC


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  21    1  0.03
  22   28  0.97

ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65


Consensus pattern (22 bp):   
ATTATTATTATTATTTTCTATT

Found at i:986 original size:25 final size:25

Alignment explanation


    Indices: 946--994  Score: 82
    Period size: 25  Copynumber: 2.0  Consensus size: 25

        936 TTTTTTAATT

                                     
        946 ATTATTATTATTTATTATTATTATA
          1 ATTATTATTATTTATTATTATTATA

                                     
        971 ATTATTATT-TTCTATTATTATTAT
          1 ATTATTATTATT-TATTATTATTAT

        995 TAGTGTAAGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  24    2  0.09
  25   21  0.91

ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65


Consensus pattern (25 bp):   
ATTATTATTATTTATTATTATTATA

Found at i:2518 original size:21 final size:22

Alignment explanation


    Indices: 2494--2543  Score: 57
    Period size: 21  Copynumber: 2.3  Consensus size: 22

       2484 GTTTTAAATT

                     *            
       2494 TAAATTTAATTATAAAA-TATA
          1 TAAATTTAAATATAAAATTATA

                 **               
       2515 TAAATACAAATATAAAATTATA
          1 TAAATTTAAATATAAAATTATA

              *    
       2537 TATATTT
          1 TAAATTT

       2544 TTAAATTTAA


Statistics
Matches: 22,  Mismatches: 6, Indels: 1
        0.76            0.21        0.03

Matches are distributed among these distances:
  21   14  0.64
  22    8  0.36

ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42


Consensus pattern (22 bp):   
TAAATTTAAATATAAAATTATA

Found at i:2871 original size:2 final size:2

Alignment explanation


    Indices: 2864--2898  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       2854 TTGAAAATTA

                                                                
       2864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2899 ATTTCCATAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.