Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1385

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: 1868
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31


Found at i:1655 original size:11 final size:11

Alignment explanation


    Indices: 1635--1686  Score: 76
    Period size: 11  Copynumber: 5.1  Consensus size: 11

       1625 GGTGATTAGG

                       
       1635 GCTT-GCGGGA
          1 GCTTGGCGGGA

                       
       1645 GCTTGGCGGGA
          1 GCTTGGCGGGA

                       
       1656 GCTTGGCGGGA
          1 GCTTGGCGGGA

                       
       1667 G---GGCGGGA
          1 GCTTGGCGGGA

                       
       1675 GCTTGGCGGGA
          1 GCTTGGCGGGA

             
       1686 G
          1 G

       1687 GTTCCTGGGT


Statistics
Matches: 38,  Mismatches: 0, Indels: 7
        0.84            0.00        0.16

Matches are distributed among these distances:
   8    8  0.21
  10    4  0.11
  11   26  0.68

ACGTcount: A:0.10, C:0.17, G:0.58, T:0.15


Consensus pattern (11 bp):   
GCTTGGCGGGA

Found at i:1673 original size:19 final size:19

Alignment explanation


    Indices: 1649--1687  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       1639 GCGGGAGCTT

                               
       1649 GGCGGGAGCTTGGCGGGAG
          1 GGCGGGAGCTTGGCGGGAG

                               
       1668 GGCGGGAGCTTGGCGGGAG
          1 GGCGGGAGCTTGGCGGGAG

             
       1687 G
          1 G

       1688 TTCCTGGGTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.10, C:0.15, G:0.64, T:0.10


Consensus pattern (19 bp):   
GGCGGGAGCTTGGCGGGAG
Done.