Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3695

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, 409

Length: 683
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36


Found at i:525 original size:11 final size:11

Alignment explanation


    Indices: 509--550  Score: 66
    Period size: 11  Copynumber: 3.7  Consensus size: 11

        499 GAAACTAGTT

                       
        509 TTTTTTTTGAA
          1 TTTTTTTTGAA

                       
        520 TTTTTTTTGAA
          1 TTTTTTTTGAA

                       *
        531 TTTTTTTTCGAG
          1 TTTTTTTT-GAA

                    
        543 TTTTTTTT
          1 TTTTTTTT

        551 CGAGAAACTA


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  11   19  0.66
  12   10  0.34

ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76


Consensus pattern (11 bp):   
TTTTTTTTGAA

Found at i:554 original size:12 final size:12

Alignment explanation


    Indices: 508--553  Score: 67
    Period size: 12  Copynumber: 3.9  Consensus size: 12

        498 GGAAACTAGT

                    *   
        508 TTTTTTTTTGAA
          1 TTTTTTTTCGAA

                        
        520 TTTTTTTT-GAA
          1 TTTTTTTTCGAA

                       *
        531 TTTTTTTTCGAG
          1 TTTTTTTTCGAA

                       
        543 TTTTTTTTCGA
          1 TTTTTTTTCGA

        554 GAAACTATTA


Statistics
Matches: 32,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  11   11  0.34
  12   21  0.66

ACGTcount: A:0.13, C:0.04, G:0.11, T:0.72


Consensus pattern (12 bp):   
TTTTTTTTCGAA

Found at i:630 original size:40 final size:40

Alignment explanation


    Indices: 552--631  Score: 115
    Period size: 40  Copynumber: 2.0  Consensus size: 40

        542 GTTTTTTTTC

                     *                       *      
        552 GAGAAACTATTATACCGTAATGCCGACAACATCGATTCTT
          1 GAGAAACTACTATACCGTAATGCCGACAACATCAATTCTT

                           *             **         
        592 GAGAAACTACTATACTGTAATGCCGACAATGTCAATTCTT
          1 GAGAAACTACTATACCGTAATGCCGACAACATCAATTCTT

        632 ACTCCAAATT


Statistics
Matches: 35,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  40   35  1.00

ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29


Consensus pattern (40 bp):   
GAGAAACTACTATACCGTAATGCCGACAACATCAATTCTT
Done.