Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2114

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: 37459
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31


Found at i:7339 original size:20 final size:20

Alignment explanation


    Indices: 7314--7355  Score: 84
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       7304 AAAGATAAGT

                                
       7314 AAAGATATAATTTGAAATAA
          1 AAAGATATAATTTGAAATAA

                                
       7334 AAAGATATAATTTGAAATAA
          1 AAAGATATAATTTGAAATAA

              
       7354 AA
          1 AA

       7356 TCTAAATAAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29


Consensus pattern (20 bp):   
AAAGATATAATTTGAAATAA

Found at i:17090 original size:23 final size:23

Alignment explanation


    Indices: 17064--17158  Score: 136
    Period size: 23  Copynumber: 4.1  Consensus size: 23

      17054 TGAAAAGTTA

                                   
      17064 GAAGAGTGAAGAGACTTGAATAT
          1 GAAGAGTGAAGAGACTTGAATAT

                      *            
      17087 GAAGAGTGAAAAGACTTGAATAT
          1 GAAGAGTGAAGAGACTTGAATAT

               *                *  
      17110 GAATAGTGAAGAGACTTGAAGAT
          1 GAAGAGTGAAGAGACTTGAATAT

               *   *     *         
      17133 GAAAAGTTAAGAGGCTTGAATAT
          1 GAAGAGTGAAGAGACTTGAATAT

               
      17156 GAA
          1 GAA

      17159 AGGATACACA


Statistics
Matches: 64,  Mismatches: 8, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  23   64  1.00

ACGTcount: A:0.45, C:0.04, G:0.28, T:0.22


Consensus pattern (23 bp):   
GAAGAGTGAAGAGACTTGAATAT

Found at i:21482 original size:23 final size:23

Alignment explanation


    Indices: 21456--21546  Score: 137
    Period size: 23  Copynumber: 4.0  Consensus size: 23

      21446 AAGTTAGAAG

                                   
      21456 AGTGAAGAGACTTGAATATGAAT
          1 AGTGAAGAGACTTGAATATGAAT

                  *                
      21479 AGTGAAAAGACTTGAATATGAAT
          1 AGTGAAGAGACTTGAATATGAAT

                            *     *
      21502 AGTGAAGAGACTTGAAGATGAAA
          1 AGTGAAGAGACTTGAATATGAAT

               *     *            
      21525 AGTTAAGAGGCTTGAATATGAA
          1 AGTGAAGAGACTTGAATATGAA

      21547 AGGATACACA


Statistics
Matches: 61,  Mismatches: 7, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  23   61  1.00

ACGTcount: A:0.45, C:0.04, G:0.26, T:0.24


Consensus pattern (23 bp):   
AGTGAAGAGACTTGAATATGAAT

Found at i:30513 original size:18 final size:19

Alignment explanation


    Indices: 30471--30515  Score: 58
    Period size: 18  Copynumber: 2.5  Consensus size: 19

      30461 GCACGACCGG

                   *           
      30471 CGAACTCCCTAAATTTGGT
          1 CGAACTCTCTAAATTTGGT

              *                
      30490 -GTACTCTCTAAATTT-GT
          1 CGAACTCTCTAAATTTGGT

                     
      30507 CGAACTCTC
          1 CGAACTCTC

      30516 CAGGAATGGC


Statistics
Matches: 22,  Mismatches: 3, Indels: 3
        0.79            0.11        0.11

Matches are distributed among these distances:
  17    2  0.09
  18   20  0.91

ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36


Consensus pattern (19 bp):   
CGAACTCTCTAAATTTGGT

Found at i:34249 original size:30 final size:29

Alignment explanation


    Indices: 34210--34279  Score: 90
    Period size: 29  Copynumber: 2.4  Consensus size: 29

      34200 TTTTGATGCA

                                           
      34210 TTTTATAATTTTTAAAAAAATTTACAAT-TT
          1 TTTTATAATTTTT-AAAAAATTTA-AATATT

                *          *             
      34240 TTTTCTAATTTTTAATAAATTTAAATATT
          1 TTTTATAATTTTTAAAAAATTTAAATATT

                        
      34269 TTTTAT-ATTTT
          1 TTTTATAATTTT

      34280 AAATAATGTT


Statistics
Matches: 36,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  28    8  0.22
  29   16  0.44
  30   12  0.33

ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60


Consensus pattern (29 bp):   
TTTTATAATTTTTAAAAAATTTAAATATT

Done.