Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1323

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: 6372
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29


Found at i:3706 original size:15 final size:15

Alignment explanation


    Indices: 3686--3716  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3676 TAAAAATGTC

                    *      
       3686 CAAAATGAGGAAGCT
          1 CAAAATGAAGAAGCT

                           
       3701 CAAAATGAAGAAGCT
          1 CAAAATGAAGAAGCT

             
       3716 C
          1 C

       3717 CAAACGAAAT


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


Consensus pattern (15 bp):   
CAAAATGAAGAAGCT

Found at i:5809 original size:20 final size:21

Alignment explanation


    Indices: 5731--5808  Score: 70
    Period size: 20  Copynumber: 3.6  Consensus size: 21

       5721 ATGTCCAAAA

                         *       
       5731 TGTATCGATACATGTTTTTG-
          1 TGTATCGATACATCTTTTTGT

                              **  * 
       5751 TGTATCGATACATCTGGAAATTCT
          1 TGTATCGATACATCT---TTTTGT

                                  
       5775 ATGTATCGATACAT-TTTTTGT
          1 -TGTATCGATACATCTTTTTGT

                         
       5796 TGTATCGATACAT
          1 TGTATCGATACAT

       5809 TGTATCGATA


Statistics
Matches: 46,  Mismatches: 7, Indels: 10
        0.73            0.11        0.16

Matches are distributed among these distances:
  20   27  0.59
  21    3  0.07
  23    2  0.04
  24    1  0.02
  25   13  0.28

ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45


Consensus pattern (21 bp):   
TGTATCGATACATCTTTTTGT

Found at i:5813 original size:13 final size:13

Alignment explanation


    Indices: 5795--5833  Score: 69
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       5785 ACATTTTTTG

                         
       5795 TTGTATCGATACA
          1 TTGTATCGATACA

                         
       5808 TTGTATCGATACA
          1 TTGTATCGATACA

            *            
       5821 CTGTATCGATACA
          1 TTGTATCGATACA

       5834 GGGTGATTAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  13   25  1.00

ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36


Consensus pattern (13 bp):   
TTGTATCGATACA
Done.