Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3017

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: 15451
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:386 original size:18 final size:16

Alignment explanation


    Indices: 355--401  Score: 58
    Period size: 18  Copynumber: 2.8  Consensus size: 16

        345 AGATAATCAT

                              
        355 AACCCAAAATTTATCCTA
          1 AACCCAAAA-TTATCC-A

                          *  
        373 AACCCTAAAATTATTCA
          1 AACCC-AAAATTATCCA

                        
        390 AACCCAAAATTA
          1 AACCCAAAATTA

        402 ATCTTATCCA


Statistics
Matches: 27,  Mismatches: 1, Indels: 4
        0.84            0.03        0.12

Matches are distributed among these distances:
  16    7  0.26
  17    6  0.22
  18   10  0.37
  19    4  0.15

ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26


Consensus pattern (16 bp):   
AACCCAAAATTATCCA

Found at i:8556 original size:21 final size:21

Alignment explanation


    Indices: 8530--8570  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8520 AGACGAGCAA

                   * *           
       8530 TACTCCACAGCAGGTGGAGTG
          1 TACTCCAAAACAGGTGGAGTG

                                
       8551 TACTCCAAAACAGGTGGAGT
          1 TACTCCAAAACAGGTGGAGT

       8571 TTGAGCAGAT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20


Consensus pattern (21 bp):   
TACTCCAAAACAGGTGGAGTG
Done.