Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2349

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: 16376
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:5279 original size:29 final size:29

Alignment explanation


    Indices: 5247--5312  Score: 78
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       5237 ATGGCCTGTG

                                  *      
       5247 ACACGGGCGTGTCTTCACACAGTCAGGCC
          1 ACACGGGCGTGTCTTCACACAGCCAGGCC

                 *  *          **      * 
       5276 ACACGAGCTTGTCTTCACATGGCCAGGTC
          1 ACACGGGCGTGTCTTCACACAGCCAGGCC

                    
       5305 ACACGGGC
          1 ACACGGGC

       5313 ATGTGTCCCT


Statistics
Matches: 30,  Mismatches: 7, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  29   30  1.00

ACGTcount: A:0.21, C:0.33, G:0.27, T:0.18


Consensus pattern (29 bp):   
ACACGGGCGTGTCTTCACACAGCCAGGCC

Found at i:9788 original size:39 final size:40

Alignment explanation


    Indices: 9607--9826  Score: 269
    Period size: 39  Copynumber: 5.7  Consensus size: 40

       9597 TTGAATGATG

                                          *   *  * * 
       9607 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA

                 *                           *       
       9647 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT-AA
          1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA

                                            *       
       9686 TCCGGGCTAAG--CCGAAGGCATTTGTGCGAGATACT-AA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA

                                                    
       9723 TCCGGG-TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA

                  *                                  
       9762 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA

                     *                
       9802 -CCGGGCTATGTCCCGAAGGCATTTG
          1 TCCGGGCTAAGTCCCGAAGGCATTTG

       9827 AACGAGGAGC


Statistics
Matches: 162,  Mismatches: 10, Indels: 16
        0.86            0.05        0.09

Matches are distributed among these distances:
  36    4  0.02
  37   32  0.20
  38   23  0.14
  39   53  0.33
  40   42  0.26
  41    8  0.05

ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25


Consensus pattern (40 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Done.