Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2325

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: 7110
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36


Found at i:2606 original size:20 final size:20

Alignment explanation


    Indices: 2559--2612  Score: 90
    Period size: 20  Copynumber: 2.7  Consensus size: 20

       2549 CATTTGAGAC

                   *            
       2559 ATGTATCAATACATTCACTT
          1 ATGTATCGATACATTCACTT

                                
       2579 ATGTATCGATACATTCACTT
          1 ATGTATCGATACATTCACTT

                     *    
       2599 ATGTATCGAGACAT
          1 ATGTATCGATACAT

       2613 GCACCAATTG


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   32  1.00

ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37


Consensus pattern (20 bp):   
ATGTATCGATACATTCACTT

Found at i:4633 original size:29 final size:29

Alignment explanation


    Indices: 4601--4660  Score: 70
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       4591 TGAAAATAAA

                                           
       4601 TATTTATAA-AT-AATATATTTAAAAAACTT
          1 TATTTATAATATAAAT-TA-TTAAAAAACTT

                 *                    *  
       4630 TATTTCTAATATAAATTATTAAAAAATTT
          1 TATTTATAATATAAATTATTAAAAAACTT

              
       4659 TA
          1 TA

       4661 AAAAACAATA


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  29   20  0.74
  30    4  0.15
  31    3  0.11

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (29 bp):   
TATTTATAATATAAATTATTAAAAAACTT

Found at i:5507 original size:16 final size:16

Alignment explanation


    Indices: 5488--5518  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       5478 GAACTTGGAA

                *           
       5488 TGACTTGAATCTAAAG
          1 TGACCTGAATCTAAAG

                           
       5504 TGACCTGAATCTAAA
          1 TGACCTGAATCTAAA

       5519 ATAACTCGAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29


Consensus pattern (16 bp):   
TGACCTGAATCTAAAG
Done.