Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1850

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: 18405
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32


Found at i:4250 original size:50 final size:54

Alignment explanation


    Indices: 4153--4281  Score: 177
    Period size: 50  Copynumber: 2.6  Consensus size: 54

       4143 ATGTGGCCCG

                                 *                                
       4153 AGGC-TCAACTCACCTCT-G-TATATGAGTTGATTTTTGAAAACAAAAATT-AA
          1 AGGCTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAAAAATTAAA

                                                         *        
       4203 AGG-TTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAA-ACAAATTAAA
          1 AGGCTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAAAAATTAAA

                                          
       4254 AGGCTT-AACTCA-CTCTCGCAATATGAGT
          1 AGGCTTCAACTCACCTCTCGCAATATGAGT

       4282 CAATTTAAAA


Statistics
Matches: 72,  Mismatches: 2, Indels: 10
        0.86            0.02        0.12

Matches are distributed among these distances:
  50   38  0.53
  51   21  0.29
  52   13  0.18

ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30


Consensus pattern (54 bp):   
AGGCTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAAAAATTAAA

Found at i:4415 original size:67 final size:70

Alignment explanation


    Indices: 4254--4423  Score: 217
    Period size: 67  Copynumber: 2.5  Consensus size: 70

       4244 ACAAATTAAA

                 *                       *  *                          **    
       4254 AGGCTTAACTCACTCTCGCAATATGAG-TCA-ATTTAAAACATAAACTAAAAGTACCTCGGCGTG
          1 AGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTAAAACATAAACTAAAAGTACCTCAACGTG

                 
       4317 CCCCG
         66 CCCCG

                                                           *                 
       4322 AGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAA-A-AAATTAAAA-TACCTCAACGT
          1 AGGCTCAACTCACTCTCGCAATATGAGTTGATTTTT-AAAACATAAACTAAAAGTACCTCAACGT

              * * 
       4384 G-TCTG
         65 GCCCCG

                                               
       4389 AGGCTCAACTCACTCTCGCAATATGAGTTGATTTT
          1 AGGCTCAACTCACTCTCGCAATATGAGTTGATTTT

       4424 CCTTGGAAAG


Statistics
Matches: 91,  Mismatches: 8, Indels: 7
        0.86            0.08        0.07

Matches are distributed among these distances:
  67   37  0.41
  68   36  0.40
  69   10  0.11
  70    4  0.04
  71    4  0.04

ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28


Consensus pattern (70 bp):   
AGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTAAAACATAAACTAAAAGTACCTCAACGTG
CCCCG

Found at i:12689 original size:15 final size:16

Alignment explanation


    Indices: 12664--12694  Score: 55
    Period size: 15  Copynumber: 2.0  Consensus size: 16

      12654 AGTATGGGAT

                            
      12664 ATGCAATGAATGAATG
          1 ATGCAATGAATGAATG

                            
      12680 ATGC-ATGAATGAATG
          1 ATGCAATGAATGAATG

      12695 CATGAATGTC


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

Matches are distributed among these distances:
  15   11  0.73
  16    4  0.27

ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26


Consensus pattern (16 bp):   
ATGCAATGAATGAATG
Done.