Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1562

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: 12314
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32


Found at i:7473 original size:9 final size:10

Alignment explanation


    Indices: 7455--7488  Score: 50
    Period size: 10  Copynumber: 3.3  Consensus size: 10

       7445 GCACTCCCCC

                      
       7455 TTTTCTTTTT
          1 TTTTCTTTTT

                      
       7465 TTTTCTTTTT
          1 TTTTCTTTTT

                *      
       7475 TTTTGTATTTT
          1 TTTTCT-TTTT

               
       7486 TTT
          1 TTT

       7489 AAATAAGTCT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  10   15  0.68
  11    7  0.32

ACGTcount: A:0.03, C:0.06, G:0.03, T:0.88


Consensus pattern (10 bp):   
TTTTCTTTTT

Found at i:9674 original size:15 final size:14

Alignment explanation


    Indices: 9646--9693  Score: 51
    Period size: 16  Copynumber: 3.2  Consensus size: 14

       9636 CCTTATTTTT

                  *       
       9646 TTTTTACACTATTC
          1 TTTTTAAACTATTC

                           
       9660 TTTTTAAACTGATTC
          1 TTTTTAAACT-ATTC

                        *   
       9675 TTTATTAATACTTTTC
          1 TTT-TTAA-ACTATTC

               
       9691 TTT
          1 TTT

       9694 CTAACCTCTA


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  14    9  0.31
  15    7  0.24
  16   10  0.34
  17    3  0.10

ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60


Consensus pattern (14 bp):   
TTTTTAAACTATTC
Done.