Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold4452

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, 318

Length: 531
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28


Found at i:189 original size:26 final size:27

Alignment explanation


    Indices: 160--212  Score: 99
    Period size: 26  Copynumber: 2.0  Consensus size: 27

        150 TATAACTTTT

                                       
        160 TTTATTTACCAAAATATAT-AAAAAAA
          1 TTTATTTACCAAAATATATCAAAAAAA

                                       
        186 TTTATTTACCAAAATATATCAAAAAAA
          1 TTTATTTACCAAAATATATCAAAAAAA

        213 CTGCAAAAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  26   19  0.73
  27    7  0.27

ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34


Consensus pattern (27 bp):   
TTTATTTACCAAAATATATCAAAAAAA

Found at i:219 original size:11 final size:11

Alignment explanation


    Indices: 205--233  Score: 51
    Period size: 10  Copynumber: 2.7  Consensus size: 11

        195 CAAAATATAT

                       
        205 CAAAAAAACTG
          1 CAAAAAAACTG

                       
        216 C-AAAAAACTG
          1 CAAAAAAACTG

                    
        226 CAAAAAAA
          1 CAAAAAAA

        234 TCAGATCGAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  10   10  0.59
  11    7  0.41

ACGTcount: A:0.69, C:0.17, G:0.07, T:0.07


Consensus pattern (11 bp):   
CAAAAAAACTG

Found at i:230 original size:9 final size:10

Alignment explanation


    Indices: 207--232  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

        197 AAATATATCA

                      
        207 AAAAAACTGC
          1 AAAAAACTGC

                      
        217 AAAAAACTGC
          1 AAAAAACTGC

                  
        227 AAAAAA
          1 AAAAAA

        233 ATCAGATCGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.69, C:0.15, G:0.08, T:0.08


Consensus pattern (10 bp):   
AAAAAACTGC

Found at i:302 original size:27 final size:27

Alignment explanation


    Indices: 270--338  Score: 104
    Period size: 27  Copynumber: 2.6  Consensus size: 27

        260 CACGCCAATA

                                        
        270 TAATTGGCGGCACCAATGGTGCCAAAAC
          1 TAATTGGCGGCACCAATGGTGCC-AAAC

             *                      *  
        298 -CATTGGCGGCACCAATGGTGCCATAC
          1 TAATTGGCGGCACCAATGGTGCCAAAC

                           
        324 TAATTGGCGGCACCA
          1 TAATTGGCGGCACCA

        339 CTCGTATTAT


Statistics
Matches: 37,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  26    3  0.08
  27   34  0.92

ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19


Consensus pattern (27 bp):   
TAATTGGCGGCACCAATGGTGCCAAAC

Found at i:474 original size:10 final size:10

Alignment explanation


    Indices: 454--493  Score: 53
    Period size: 11  Copynumber: 3.7  Consensus size: 10

        444 ATTGGCGCGG

                       
        454 AAAGAAGAGAA
          1 AAAG-AGAGAA

                      
        465 AAAGAGAGAA
          1 AAAGAGAGAA

                       
        475 AAAGAGGAGAA
          1 AAAGA-GAGAA

                    
        486 AAATGAGA
          1 AAA-GAGA

        494 TATTTTTTTA


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  10   11  0.41
  11   14  0.52
  12    2  0.07

ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03


Consensus pattern (10 bp):   
AAAGAGAGAA
Done.