Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3394

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: 18872
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31


Found at i:723 original size:40 final size:40

Alignment explanation


    Indices: 656--834  Score: 225
    Period size: 40  Copynumber: 4.5  Consensus size: 40

        646 CGAATGATAC

                  *   *         *                   
        656 CCGGGCGAAGTCCCGAAGGCTTTTGTGCTAGCGACTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATAT

             *  *      *                *  ***      
        696 CTGGACTAAGATCCGAAGGCATTTGTGCGAGTTTCTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATAT

                                                    
        736 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATAT

                       *            *      *   *    
        776 CCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGACCATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATAT

                                
        815 CCGGGCTAAGACCCGAAGGC
          1 CCGGGCTAAGACCCGAAGGC

        835 CTTGTGTGAG


Statistics
Matches: 116,  Mismatches: 22, Indels: 2
        0.83            0.16        0.01

Matches are distributed among these distances:
  39   35  0.30
  40   81  0.70

ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24


Consensus pattern (40 bp):   
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATAT

Found at i:831 original size:79 final size:80

Alignment explanation


    Indices: 656--834  Score: 261
    Period size: 80  Copynumber: 2.2  Consensus size: 80

        646 CGAATGATAC

                  *   *         *                    *                      *
        656 CCGGGCGAAGTCCCGAAGGCTTTTGTGCTAGCGACTATATCTGGACTAAGATCCGAAGGCATTTG
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGACTAAGATCCGAAGGCATTTA

                   ** *    
        721 TGCGAGTTTCTATAT
         66 TGCGAGTGACCATAT

                                                        *                    
        736 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAG-TCCGAAGGCATTTA
          1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGACTAAGATCCGAAGGCATTTA

               *           
        800 TGCTAGTGACCATAT
         66 TGCGAGTGACCATAT

                                
        815 CCGGGCTAAGACCCGAAGGC
          1 CCGGGCTAAGACCCGAAGGC

        835 CTTGTGTGAG


Statistics
Matches: 89,  Mismatches: 10, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  79   44  0.49
  80   45  0.51

ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24


Consensus pattern (80 bp):   
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGACTAAGATCCGAAGGCATTTA
TGCGAGTGACCATAT

Found at i:854 original size:39 final size:39

Alignment explanation


    Indices: 656--870  Score: 204
    Period size: 40  Copynumber: 5.5  Consensus size: 39

        646 CGAATGATAC

                  *   *         *          *        
        656 CCGGGCGAAGTCCCGAAGGCTTTTGTGCTAGCGACTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGC-AGTGACTATAT

             *  *      *                    **      
        696 CTGGACTAAGATCCGAAGGCATTTGTGCGAGTTTCTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGC-AGTGACTATAT

                                           *        
        736 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGC-AGTGACTATAT

                       *            *          *    
        776 CCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGACCATAT
          1 CCGGGCTAAGACCCGAAGGCATTTGTGC-AGTGACTATAT

                                *            **     
        815 CCGGGCTAAGACCCGAAGGCCTTGTGTG-AGTGGTTATAT
          1 CCGGGCTAAGACCCGAAGGCATT-TGTGCAGTGACTATAT

                               
        854 CC-GGCTAA-ATCCCGAAG
          1 CCGGGCTAAGA-CCCGAAG

        871 ATACTTGGGT


Statistics
Matches: 145,  Mismatches: 27, Indels: 8
        0.81            0.15        0.04

Matches are distributed among these distances:
  37    1  0.01
  38   13  0.09
  39   45  0.31
  40   83  0.57
  41    3  0.02

ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25


Consensus pattern (39 bp):   
CCGGGCTAAGACCCGAAGGCATTTGTGCAGTGACTATAT

Found at i:7628 original size:29 final size:30

Alignment explanation


    Indices: 7572--7630  Score: 93
    Period size: 29  Copynumber: 2.0  Consensus size: 30

       7562 TTCCCAAGCC

                                          
       7572 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
          1 TAGGGGCAAAAGTGTAATTATGCAAAAGTT

                               *   *      
       7602 TAGGGGCAAAA-TGTAATTTTGCCAAAGTT
          1 TAGGGGCAAAAGTGTAATTATGCAAAAGTT

       7631 CGTATTAAGG


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  29   16  0.59
  30   11  0.41

ACGTcount: A:0.37, C:0.08, G:0.25, T:0.29


Consensus pattern (30 bp):   
TAGGGGCAAAAGTGTAATTATGCAAAAGTT

Found at i:14151 original size:14 final size:14

Alignment explanation


    Indices: 14132--14162  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      14122 AGCAGAAAGT

                       *  
      14132 AAAAGTAATCCGTG
          1 AAAAGTAATCCATG

                          
      14146 AAAAGTAATCCATG
          1 AAAAGTAATCCATG

               
      14160 AAA
          1 AAA

      14163 GTCTGAAAGC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.52, C:0.13, G:0.16, T:0.19


Consensus pattern (14 bp):   
AAAAGTAATCCATG
Done.