Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold201

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: 841227
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30

Warning! 75646 characters in sequence are not A, C, G, or T


File 6 of 6

Found at i:828575 original size:20 final size:21

Alignment explanation


    Indices: 828550--828602  Score: 74
    Period size: 20  Copynumber: 2.6  Consensus size: 21

     828540 ACAAAGCCAA

                           *     
     828550 TGTATCGATACAAT-TTTTGG
          1 TGTATCGATACAATACTTTGG

                                 
     828570 TGTATCGATAC-ATACTTTGG
          1 TGTATCGATACAATACTTTGG

            *            
     828590 GGTATCGATACAA
          1 TGTATCGATACAA

     828603 GTTTGGCTAC


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  19    2  0.07
  20   26  0.90
  21    1  0.03

ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38


Consensus pattern (21 bp):   
TGTATCGATACAATACTTTGG

Found at i:830629 original size:15 final size:15

Alignment explanation


    Indices: 830609--830639  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

     830599 ATTTCGTTAG

                   *       
     830609 GAGCTTCTTCATTTT
          1 GAGCTTCCTCATTTT

                           
     830624 GAGCTTCCTCATTTT
          1 GAGCTTCCTCATTTT

             
     830639 G
          1 G

     830640 GACATTTTTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48


Consensus pattern (15 bp):   
GAGCTTCCTCATTTT

Found at i:832455 original size:21 final size:22

Alignment explanation


    Indices: 832429--832469  Score: 66
    Period size: 21  Copynumber: 1.9  Consensus size: 22

     832419 ATGCAAGTTT

                           *      
     832429 TTATTTTTC-TTAGCTAACTCA
          1 TTATTTTTCATTAGCCAACTCA

                                
     832450 TTATTTTTCATTAGCCAACT
          1 TTATTTTTCATTAGCCAACT

     832470 TCTTTAGTTC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    9  0.50
  22    9  0.50

ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51


Consensus pattern (22 bp):   
TTATTTTTCATTAGCCAACTCA

Found at i:834711 original size:13 final size:13

Alignment explanation


    Indices: 834693--834718  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

     834683 CAATTATTTG

                         
     834693 TGTATCGATACAT
          1 TGTATCGATACAT

                         
     834706 TGTATCGATACAT
          1 TGTATCGATACAT

     834719 ACTTGGTGTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38


Consensus pattern (13 bp):   
TGTATCGATACAT

Found at i:834733 original size:32 final size:33

Alignment explanation


    Indices: 834673--834736  Score: 96
    Period size: 32  Copynumber: 2.0  Consensus size: 33

     834663 TACAAGCCAA

                              *              
     834673 TGTATCGATACAATTATTTGTGTATCGATACAT
          1 TGTATCGATACAATTATTGGTGTATCGATACAT

                                             
     834706 TGTATCGATAC-A-TACTTGGTGTATCGATACA
          1 TGTATCGATACAATTA-TTGGTGTATCGATACA

     834737 AGTTTGGCTG


Statistics
Matches: 29,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  31    2  0.07
  32   16  0.55
  33   11  0.38

ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39


Consensus pattern (33 bp):   
TGTATCGATACAATTATTGGTGTATCGATACAT

Found at i:837287 original size:13 final size:13

Alignment explanation


    Indices: 837269--837294  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

     837259 ATAATCACCC

                         
     837269 TGTATCGATACAA
          1 TGTATCGATACAA

                         
     837282 TGTATCGATACAA
          1 TGTATCGATACAA

     837295 AGAAAAATGT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31


Consensus pattern (13 bp):   
TGTATCGATACAA

Found at i:839388 original size:15 final size:15

Alignment explanation


    Indices: 839368--839398  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

     839358 ATTTCGTTTG

                   *       
     839368 GAGCTTCTTCATTTT
          1 GAGCTTCCTCATTTT

                           
     839383 GAGCTTCCTCATTTT
          1 GAGCTTCCTCATTTT

             
     839398 G
          1 G

     839399 GACATTTTTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48


Consensus pattern (15 bp):   
GAGCTTCCTCATTTT

Done.