Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold573

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: 4623
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34


Found at i:700 original size:11 final size:11

Alignment explanation


    Indices: 684--708  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

        674 GACATAAAAA

                       
        684 ATAATATAAAT
          1 ATAATATAAAT

                       
        695 ATAATATAAAT
          1 ATAATATAAAT

               
        706 ATA
          1 ATA

        709 TAAATTTCAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (11 bp):   
ATAATATAAAT

Found at i:1626 original size:20 final size:20

Alignment explanation


    Indices: 1598--1672  Score: 87
    Period size: 20  Copynumber: 3.8  Consensus size: 20

       1588 TCATACCCTG

                                
       1598 ATGTATCGATACATTTTTCA
          1 ATGTATCGATACATTTTTCA

              *           * * * 
       1618 ATATATCGATACATGTATGA
          1 ATGTATCGATACATTTTTCA

                       *   * *  
       1638 ATGTATCGATATATTCTACA
          1 ATGTATCGATACATTTTTCA

                           
       1658 ATGTATCGATACATT
          1 ATGTATCGATACATT

       1673 ATGTGTTTTT


Statistics
Matches: 43,  Mismatches: 12, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  20   43  1.00

ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40


Consensus pattern (20 bp):   
ATGTATCGATACATTTTTCA

Found at i:1665 original size:40 final size:39

Alignment explanation


    Indices: 1598--1675  Score: 111
    Period size: 40  Copynumber: 2.0  Consensus size: 39

       1588 TCATACCCTG

                           * *                      
       1598 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
          1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA

                       *          *               
       1638 ATGTATCGATATATTCTACAATGTATCGATACATTATG
          1 ATGTATCGATACATTCTACAATATATCGATACATTATG

       1676 TGTTTTTTAC


Statistics
Matches: 34,  Mismatches: 4, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  39    4  0.12
  40   30  0.88

ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40


Consensus pattern (39 bp):   
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Done.