Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2471

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: 183824
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


File 2 of 2

Found at i:174115 original size:33 final size:33

Alignment explanation


    Indices: 174073--174139  Score: 98
    Period size: 33  Copynumber: 2.0  Consensus size: 33

     174063 GCCAAGGAAA

                         ***                 
     174073 TGTATCGATACATTTTTCTGTGTATCGATACAT
          1 TGTATCGATACATGGATCTGTGTATCGATACAT

                               *             
     174106 TGTATCGATACATGGATCTTTGTATCGATACAT
          1 TGTATCGATACATGGATCTGTGTATCGATACAT

             
     174139 T
          1 T

     174140 TGGAAATTTA


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   30  1.00

ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43


Consensus pattern (33 bp):   
TGTATCGATACATGGATCTGTGTATCGATACAT

Found at i:176707 original size:51 final size:51

Alignment explanation


    Indices: 176645--176815  Score: 173
    Period size: 51  Copynumber: 3.3  Consensus size: 51

     176635 TTATTTCTGA

                               *               * *             
     176645 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTTATAATC
          1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTTATAATC

                              *           *  *                    
     176696 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTT-TAATC
          1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-T--TTATAATC

                 *  *    **            *                 * *    
     176749 GGGGACACGCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
          1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTTATAATC

             *             
     176801 GAGGATACTCCAACC
          1 GGGGATACTCCAACC

     176816 TCGTTATTTC


Statistics
Matches: 94,  Mismatches: 21, Indels: 9
        0.76            0.17        0.07

Matches are distributed among these distances:
  51   37  0.39
  52   15  0.16
  53   29  0.31
  54   13  0.14

ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32


Consensus pattern (51 bp):   
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTTATAATC

Found at i:176834 original size:28 final size:28

Alignment explanation


    Indices: 176798--176879  Score: 96
    Period size: 28  Copynumber: 2.9  Consensus size: 28

     176788 ATTTTTCACA

                *                       
     176798 ATCGAGGATACTCCAACCTCGTTATTTC
          1 ATCGGGGATACTCCAACCTCGTTATTTC

                              *     *   
     176826 ATCGGGGATACTCCAACCCCGTTACTTC
          1 ATCGGGGATACTCCAACCTCGTTATTTC

                      *                 
     176854 --CGAGGGAACACTCCAACCTCGTTATT
          1 ATCG-GGG-ATACTCCAACCTCGTTATT

     176880 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

Found at i:182941 original size:20 final size:19

Alignment explanation


    Indices: 182912--182955  Score: 52
    Period size: 19  Copynumber: 2.3  Consensus size: 19

     182902 TCCCAAATGT

                 *              
     182912 ATCGATACAATATTCTTTGC
          1 ATCGACACAA-ATTCTTTGC

                      *       *
     182932 ATCGACACAAGTTCTTTGT
          1 ATCGACACAAATTCTTTGC

                 
     182951 ATCGA
          1 ATCGA

     182956 TACATGAGTT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  19   12  0.57
  20    9  0.43

ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36


Consensus pattern (19 bp):   
ATCGACACAAATTCTTTGC

Done.