Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1190

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: 8464
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30


Found at i:323 original size:13 final size:13

Alignment explanation


    Indices: 305--330  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        295 TACACAAAGT

                         
        305 ATGTATCGATACA
          1 ATGTATCGATACA

                         
        318 ATGTATCGATACA
          1 ATGTATCGATACA

        331 CAAAAAAATT


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):   
ATGTATCGATACA

Found at i:349 original size:34 final size:32

Alignment explanation


    Indices: 287--351  Score: 94
    Period size: 32  Copynumber: 2.0  Consensus size: 32

        277 TAGCCAAACT

                            **              
        287 TGTATCGATACACAAAGTATGTATCGATACAA
          1 TGTATCGATACACAAAAAATGTATCGATACAA

                                             
        319 TGTATCGATACACAAAAAAATTGTATCGATACA
          1 TGTATCGATACAC-AAAAAA-TGTATCGATACA

        352 TTGGCTTGTA


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  32   13  0.45
  33    4  0.14
  34   12  0.41

ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28


Consensus pattern (32 bp):   
TGTATCGATACACAAAAAATGTATCGATACAA

Found at i:4386 original size:15 final size:15

Alignment explanation


    Indices: 4366--4404  Score: 60
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       4356 GATAAATGTC

                    *      
       4366 CAAAATGAGGAAGCT
          1 CAAAATGAAGAAGCT

                           
       4381 CAAAATGAAGAAGCT
          1 CAAAATGAAGAAGCT

             *       
       4396 CCAAATGAA
          1 CAAAATGAA

       4405 ATTGATGAAC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13


Consensus pattern (15 bp):   
CAAAATGAAGAAGCT

Found at i:6478 original size:13 final size:13

Alignment explanation


    Indices: 6460--6485  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       6450 ACATTTTTCT

                         
       6460 TTGTATCGATACA
          1 TTGTATCGATACA

                         
       6473 TTGTATCGATACA
          1 TTGTATCGATACA

       6486 GGGTGATTAT


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):   
TTGTATCGATACA
Done.