Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1321

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: 2032
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.29

Warning! 237 characters in sequence are not A, C, G, or T


Found at i:1022 original size:38 final size:38

Alignment explanation


    Indices: 971--1054  Score: 159
    Period size: 38  Copynumber: 2.2  Consensus size: 38

        961 CATTGTAAAT

                  *                               
        971 TTGAAGAAAATTCCTCCCTCCAATGAGTATTTTCCTGC
          1 TTGAAGGAAATTCCTCCCTCCAATGAGTATTTTCCTGC

                                                  
       1009 TTGAAGGAAATTCCTCCCTCCAATGAGTATTTTCCTGC
          1 TTGAAGGAAATTCCTCCCTCCAATGAGTATTTTCCTGC

                    
       1047 TTGAAGGA
          1 TTGAAGGA

       1055 GAAGGAACAG


Statistics
Matches: 45,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  38   45  1.00

ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33


Consensus pattern (38 bp):   
TTGAAGGAAATTCCTCCCTCCAATGAGTATTTTCCTGC

Found at i:1543 original size:13 final size:13

Alignment explanation


    Indices: 1513--1542  Score: 53
    Period size: 13  Copynumber: 2.4  Consensus size: 13

       1503 ATTGAGTTTA

                         
       1513 ATTTTAAGGCACT
          1 ATTTTAAGGCACT

                         
       1526 ATTTTAAGGCACT
          1 ATTTTAAGGCACT

                 
       1539 -TTTT
          1 ATTTT

       1543 TGGTATATAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12    4  0.24
  13   13  0.76

ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47


Consensus pattern (13 bp):   
ATTTTAAGGCACT

Found at i:1819 original size:21 final size:21

Alignment explanation


    Indices: 1789--1846  Score: 89
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       1779 ATAGGAGCCA

                 *               
       1789 ACCTAACTGCGAGGTCCTCTC
          1 ACCTATCTGCGAGGTCCTCTC

                           *     
       1810 ACCTATCTGCGAGGTGCTCTC
          1 ACCTATCTGCGAGGTCCTCTC

                   *        
       1831 ACCTATCGGCGAGGTC
          1 ACCTATCTGCGAGGTC

       1847 TCCTNNNNNN


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   33  1.00

ACGTcount: A:0.17, C:0.34, G:0.24, T:0.24


Consensus pattern (21 bp):   
ACCTATCTGCGAGGTCCTCTC
Done.