Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2391

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: 10953
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:1217 original size:2 final size:2

Alignment explanation


    Indices: 1210--1237  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       1200 GATTTTAAAT

                                                     
       1210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1238 ACACTTTCAG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:2439 original size:24 final size:25

Alignment explanation


    Indices: 2412--2471  Score: 70
    Period size: 24  Copynumber: 2.5  Consensus size: 25

       2402 TAAAAAAATT

                                  *  
       2412 AATAATAATTAAATT-ATATTTTTA
          1 AATAATAATTAAATTAATATTTATA

                   *  *              
       2436 AATAA-ATTTTAATTAATATTTATA
          1 AATAATAATTAAATTAATATTTATA

                *       
       2460 AATATTAATTAA
          1 AATAATAATTAA

       2472 CCGAATATTC


Statistics
Matches: 28,  Mismatches: 6, Indels: 3
        0.76            0.16        0.08

Matches are distributed among these distances:
  23    7  0.25
  24   17  0.61
  25    4  0.14

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (25 bp):   
AATAATAATTAAATTAATATTTATA

Found at i:2864 original size:2 final size:2

Alignment explanation


    Indices: 2852--2891  Score: 53
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       2842 AAGCTATTAA

                                           *              *            
       2852 AT AT GAT AT AT AT AT AT AT AT GT AT AT AT AT GT AT AT AT A
          1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2892 CACACATATT


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
   2   31  0.94
   3    2  0.06

ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:4662 original size:28 final size:28

Alignment explanation


    Indices: 4622--4699  Score: 77
    Period size: 28  Copynumber: 2.7  Consensus size: 28

       4612 TTAAATATTT

                    *                    
       4622 AATTTAAAATTAATTATTAA-TATACAAA
          1 AATTTAAATTTAATTATTAATTATA-AAA

                 *       *   *         *
       4650 AATTTTAATTTAAATATAAATTATAAAT
          1 AATTTAAATTTAATTATTAATTATAAAA

                                  
       4678 AATTTAAAATTTAATTAATTAA
          1 AATTT-AAATTTAATT-ATTAA

       4700 AAATAATACC


Statistics
Matches: 39,  Mismatches: 8, Indels: 4
        0.76            0.16        0.08

Matches are distributed among these distances:
  28   23  0.59
  29   12  0.31
  30    4  0.10

ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44


Consensus pattern (28 bp):   
AATTTAAATTTAATTATTAATTATAAAA

Found at i:4691 original size:34 final size:33

Alignment explanation


    Indices: 4602--4693  Score: 98
    Period size: 34  Copynumber: 2.7  Consensus size: 33

       4592 TACTTGAATC

                                           *  
       4602 TTATAAA-ATATTAAATATTTAATTTAAAATTAA
          1 TTATAAATATATTAAA-ATTTAATTTAAAATAAA

                *      **                      
       4635 TTATTAATATACAAAAATTTTAATTTAAATATAAA
          1 TTATAAATATATTAAAA-TTTAATTTAAA-ATAAA

                                     
       4670 TTATAAATA-ATTTAAAATTTAATT
          1 TTATAAATATA-TTAAAATTTAATT

       4694 AATTAAAAAT


Statistics
Matches: 48,  Mismatches: 7, Indels: 7
        0.77            0.11        0.11

Matches are distributed among these distances:
  33    7  0.15
  34   25  0.52
  35   16  0.33

ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46


Consensus pattern (33 bp):   
TTATAAATATATTAAAATTTAATTTAAAATAAA

Found at i:6052 original size:2 final size:2

Alignment explanation


    Indices: 6047--6089  Score: 86
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       6037 GTACAGTTTA

                                                                          
       6047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

             
       6089 A
          1 A

       6090 ACTTTAAAAT


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   41  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:7871 original size:7 final size:7

Alignment explanation


    Indices: 7859--7890  Score: 64
    Period size: 7  Copynumber: 4.6  Consensus size: 7

       7849 TACTCTCAGT

                   
       7859 AATGGAA
          1 AATGGAA

                   
       7866 AATGGAA
          1 AATGGAA

                   
       7873 AATGGAA
          1 AATGGAA

                   
       7880 AATGGAA
          1 AATGGAA

                
       7887 AATG
          1 AATG

       7891 ACAAGCAGTG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   25  1.00

ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16


Consensus pattern (7 bp):   
AATGGAA

Done.