Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2462

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: 11514
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36


Found at i:2410 original size:16 final size:16

Alignment explanation


    Indices: 2369--2411  Score: 52
    Period size: 16  Copynumber: 2.7  Consensus size: 16

       2359 TTTGGGTCAT

                      *     
       2369 TTTCGAGTTCAGATCG
          1 TTTCGAGTTCGGATCG

                           * 
       2385 TTTC-AGGTTCGGATTG
          1 TTTCGA-GTTCGGATCG

                       
       2401 TTTCGAGTTCG
          1 TTTCGAGTTCG

       2412 AGTTATTTCG


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  15    1  0.04
  16   21  0.91
  17    1  0.04

ACGTcount: A:0.14, C:0.16, G:0.28, T:0.42


Consensus pattern (16 bp):   
TTTCGAGTTCGGATCG

Found at i:8358 original size:6 final size:6

Alignment explanation


    Indices: 8337--8370  Score: 54
    Period size: 6  Copynumber: 6.0  Consensus size: 6

       8327 GTTTTCTCTA

                                                     
       8337 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT
          1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT

       8371 GTTTGATTAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   5   10  0.36
   6   18  0.64

ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82


Consensus pattern (6 bp):   
TTTTAT

Found at i:10480 original size:15 final size:15

Alignment explanation


    Indices: 10460--10488  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      10450 ATCTAATACT

                           
      10460 AATAGAATAGAAAAA
          1 AATAGAATAGAAAAA

                          
      10475 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

      10489 TACTAATATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14


Consensus pattern (15 bp):   
AATAGAATAGAAAAA
Done.