Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold682

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: 119999
ACGTcount: A:0.04, C:0.02, G:0.02, T:0.04

Warning! 105716 characters in sequence are not A, C, G, or T


Found at i:38518 original size:14 final size:13

Alignment explanation


    Indices: 38487--38520  Score: 59
    Period size: 13  Copynumber: 2.6  Consensus size: 13

      38477 TACACCTTGG

                         
      38487 ATTTTTTTTTCAA
          1 ATTTTTTTTTCAA

                  *      
      38500 ATTTTTATTTCAA
          1 ATTTTTTTTTCAA

                    
      38513 ATTTTTTT
          1 ATTTTTTT

      38521 ACAATCACTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71


Consensus pattern (13 bp):   
ATTTTTTTTTCAA

Found at i:47146 original size:17 final size:16

Alignment explanation


    Indices: 47116--47157  Score: 57
    Period size: 17  Copynumber: 2.5  Consensus size: 16

      47106 GTATACAATA

                            
      47116 TTTTTTTTCAATTTTT
          1 TTTTTTTTCAATTTTT

                      *      
      47132 TTTTCTTTTCGATTTTT
          1 TTTT-TTTTCAATTTTT

                     
      47149 TTTATTTTT
          1 TTT-TTTTT

      47158 TTTCAATTTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  16    4  0.17
  17   18  0.78
  18    1  0.04

ACGTcount: A:0.10, C:0.07, G:0.02, T:0.81


Consensus pattern (16 bp):   
TTTTTTTTCAATTTTT

Found at i:47150 original size:20 final size:20

Alignment explanation


    Indices: 47114--47170  Score: 75
    Period size: 20  Copynumber: 3.0  Consensus size: 20

      47104 CCGTATACAA

                                
      47114 TATTTTTTTTCAA--TTTTT
          1 TATTTTTTTTCAATTTTTTT

                 *     *        
      47132 T-TTTCTTTTCGATTTTTTT
          1 TATTTTTTTTCAATTTTTTT

                                
      47151 TATTTTTTTTCAATTTTTTT
          1 TATTTTTTTTCAATTTTTTT

      47171 GAAACTACAA


Statistics
Matches: 32,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  17    9  0.28
  18    1  0.03
  19    6  0.19
  20   16  0.50

ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79


Consensus pattern (20 bp):   
TATTTTTTTTCAATTTTTTT

Found at i:80279 original size:47 final size:48

Alignment explanation


    Indices: 80190--80288  Score: 146
    Period size: 47  Copynumber: 2.1  Consensus size: 48

      80180 AAAATCAGCT

                          *      *   *    *    *            
      80190 GCAGCAAAGACAAGTTTAATGTCTAGATTCGGCTGGACAAATTAAATA
          1 GCAGCAAAGACAAGATTAATGACTAAATTCAGCTGAACAAATTAAATA

                                                            
      80238 GCAGCAAAGACAA-ATTAATGACTAAATTCAGCTGAACAAATTAAATA
          1 GCAGCAAAGACAAGATTAATGACTAAATTCAGCTGAACAAATTAAATA

                
      80285 GCAG
          1 GCAG

      80289 TAGCTAATAA


Statistics
Matches: 46,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  47   33  0.72
  48   13  0.28

ACGTcount: A:0.44, C:0.15, G:0.18, T:0.22


Consensus pattern (48 bp):   
GCAGCAAAGACAAGATTAATGACTAAATTCAGCTGAACAAATTAAATA

Found at i:119267 original size:18 final size:17

Alignment explanation


    Indices: 119227--119267  Score: 55
    Period size: 18  Copynumber: 2.4  Consensus size: 17

     119217 GAAGAAGAAA

                             
     119227 ACAAAAAGATGAGTGAT
          1 ACAAAAAGATGAGTGAT

             *                
     119244 AAAAAAAGATAGAGTGAT
          1 ACAAAAAGAT-GAGTGAT

            *     
     119262 TCAAAA
          1 ACAAAA

     119268 GAAAAAGAAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  17    9  0.45
  18   11  0.55

ACGTcount: A:0.59, C:0.05, G:0.20, T:0.17


Consensus pattern (17 bp):   
ACAAAAAGATGAGTGAT

Found at i:119912 original size:20 final size:20

Alignment explanation


    Indices: 119887--119933  Score: 60
    Period size: 20  Copynumber: 2.4  Consensus size: 20

     119877 AGCTCGTTTC

                          *      
     119887 CAGCTCACTT-GAGCTCAAGT
          1 CAGCTCA-TTCGAGATCAAGT

                              * 
     119907 CAGCTCATTCGAGATCAATT
          1 CAGCTCATTCGAGATCAAGT

                   
     119927 CAGCTCA
          1 CAGCTCA

     119934 ATTTTAACCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  19    2  0.08
  20   22  0.92

ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26


Consensus pattern (20 bp):   
CAGCTCATTCGAGATCAAGT
Done.