Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2545

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: 5893
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32


Found at i:53 original size:13 final size:13

Alignment explanation


    Indices: 35--60  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

         25 ATTTTTTCTG

                         
         35 TGTATCGATACAT
          1 TGTATCGATACAT

                         
         48 TGTATCGATACAT
          1 TGTATCGATACAT

         61 GGATCTTTGT


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:2597 original size:28 final size:27

Alignment explanation


    Indices: 2530--2602  Score: 94
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       2520 CTTCACAATC

                 *                    *
       2530 GGGGACACTCCAACCCCGTTAATCATC
          1 GGGGATACTCCAACCCCGTTAATCATA

                                  *      
       2557 GGGGATACTCCAACCCCGTTATTTC-TGA
          1 GGGGATACTCCAACCCCGTTA-ATCAT-A

                              
       2585 GGGGATACTCCAACCCCG
          1 GGGGATACTCCAACCCCG

       2603 ACTTTATTTT


Statistics
Matches: 41,  Mismatches: 3, Indels: 3
        0.87            0.06        0.06

Matches are distributed among these distances:
  27   21  0.51
  28   20  0.49

ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21


Consensus pattern (27 bp):   
GGGGATACTCCAACCCCGTTAATCATA

Found at i:2647 original size:51 final size:51

Alignment explanation


    Indices: 2585--2755  Score: 198
    Period size: 51  Copynumber: 3.3  Consensus size: 51

       2575 TTATTTCTGA

                               *               * *             
       2585 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
          1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC

                              *           *  *          *  *     
       2636 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
          1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC

                         **            *                   *    
       2689 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
          1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC

             *             
       2741 GAGGATACTCCAACC
          1 GGGGATACTCCAACC

       2756 TCGTTATTTC


Statistics
Matches: 97,  Mismatches: 20, Indels: 5
        0.80            0.16        0.04

Matches are distributed among these distances:
  51   36  0.37
  52   18  0.19
  53   32  0.33
  54   11  0.11

ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33


Consensus pattern (51 bp):   
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC

Found at i:2774 original size:28 final size:28

Alignment explanation


    Indices: 2738--2819  Score: 96
    Period size: 28  Copynumber: 2.9  Consensus size: 28

       2728 ATTTTTCACA

                *                       
       2738 ATCGAGGATACTCCAACCTCGTTATTTC
          1 ATCGGGGATACTCCAACCTCGTTATTTC

                              *     *   
       2766 ATCGGGGATACTCCAACCCCGTTACTTC
          1 ATCGGGGATACTCCAACCTCGTTATTTC

                      *                 
       2794 --CGAGGGAACACTCCAACCTCGTTATT
          1 ATCG-GGG-ATACTCCAACCTCGTTATT

       2820 ATCTCCAAAA


Statistics
Matches: 46,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  26    2  0.04
  27    3  0.07
  28   41  0.89

ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27


Consensus pattern (28 bp):   
ATCGGGGATACTCCAACCTCGTTATTTC
Done.