Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold599

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: 5439
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37


Found at i:756 original size:15 final size:15

Alignment explanation


    Indices: 736--766  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        726 ATTTCGTTTG

                   *       
        736 GAGCTTCTTCATTTT
          1 GAGCTTCCTCATTTT

                           
        751 GAGCTTCCTCATTTT
          1 GAGCTTCCTCATTTT

             
        766 G
          1 G

        767 GACATTTTTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48


Consensus pattern (15 bp):   
GAGCTTCCTCATTTT

Found at i:4844 original size:13 final size:13

Alignment explanation


    Indices: 4826--4851  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       4816 CAATTTTTTG

                         
       4826 TGTATCGATACAT
          1 TGTATCGATACAT

                         
       4839 TGTATCGATACAT
          1 TGTATCGATACAT

       4852 ACTTGCTGTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:4936 original size:20 final size:20

Alignment explanation


    Indices: 4911--4984  Score: 85
    Period size: 20  Copynumber: 3.6  Consensus size: 20

       4901 CATCTGTTTT

                                
       4911 ATGTATCGATACATTGCAAC
          1 ATGTATCGATACATTGCAAC

                             **** 
       4931 ATGTATCGATACAATCTTTTTC
          1 ATGTATCGATAC-AT-TGCAAC

                                
       4953 ATGTATCGATACATTGCAAC
          1 ATGTATCGATACATTGCAAC

              *         
       4973 ATTTATCGATAC
          1 ATGTATCGATAC

       4985 TTGAATTGTG


Statistics
Matches: 43,  Mismatches: 9, Indels: 4
        0.77            0.16        0.07

Matches are distributed among these distances:
  20   25  0.58
  21    4  0.09
  22   14  0.33

ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36


Consensus pattern (20 bp):   
ATGTATCGATACATTGCAAC

Found at i:4965 original size:42 final size:41

Alignment explanation


    Indices: 4890--4984  Score: 156
    Period size: 42  Copynumber: 2.3  Consensus size: 41

       4880 CTGCCAAGAA

                                                     
       4890 ATGTATCGATACATCTGTTTTATGTATCGATACATTGCAAC
          1 ATGTATCGATACATCTGTTTTATGTATCGATACATTGCAAC

                                                       
       4931 ATGTATCGATACAATCT-TTTTCATGTATCGATACATTGCAAC
          1 ATGTATCGATAC-ATCTGTTTT-ATGTATCGATACATTGCAAC

              *         
       4973 ATTTATCGATAC
          1 ATGTATCGATAC

       4985 TTGAATTGTG


Statistics
Matches: 51,  Mismatches: 1, Indels: 3
        0.93            0.02        0.05

Matches are distributed among these distances:
  41   16  0.31
  42   35  0.69

ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39


Consensus pattern (41 bp):   
ATGTATCGATACATCTGTTTTATGTATCGATACATTGCAAC
Done.