Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3734

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: 42630
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:3576 original size:64 final size:65

Alignment explanation


    Indices: 3497--3626  Score: 253
    Period size: 65  Copynumber: 2.0  Consensus size: 65

       3487 TGGGACTTGG

                                                                             
       3497 GACTGTTAGAAGTAGATTAAGATTT-AAATAGATAAAAACATAAAGAGAGGCTGATAATGGATTT
          1 GACTGTTAGAAGTAGATTAAGATTTAAAATAGATAAAAACATAAAGAGAGGCTGATAATGGATTT

                                                                             
       3561 GACTGTTAGAAGTAGATTAAGATTTAAAATAGATAAAAACATAAAGAGAGGCTGATAATGGATTT
          1 GACTGTTAGAAGTAGATTAAGATTTAAAATAGATAAAAACATAAAGAGAGGCTGATAATGGATTT

             
       3626 G
          1 G

       3627 GACTTTCGGA


Statistics
Matches: 65,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  64   25  0.38
  65   40  0.62

ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28


Consensus pattern (65 bp):   
GACTGTTAGAAGTAGATTAAGATTTAAAATAGATAAAAACATAAAGAGAGGCTGATAATGGATTT

Found at i:17880 original size:18 final size:18

Alignment explanation


    Indices: 17857--17897  Score: 82
    Period size: 18  Copynumber: 2.3  Consensus size: 18

      17847 TCAGGGGGAA

                              
      17857 TGTCAAGCCAAATTTGCT
          1 TGTCAAGCCAAATTTGCT

                              
      17875 TGTCAAGCCAAATTTGCT
          1 TGTCAAGCCAAATTTGCT

                 
      17893 TGTCA
          1 TGTCA

      17898 TTTGGATTGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   23  1.00

ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34


Consensus pattern (18 bp):   
TGTCAAGCCAAATTTGCT

Found at i:18406 original size:59 final size:58

Alignment explanation


    Indices: 18314--18428  Score: 221
    Period size: 59  Copynumber: 2.0  Consensus size: 58

      18304 ACTTTCACAT

                                                                       
      18314 CATACATTCAGTCCTGAAATTAGAGTTATGTTTCACATTTAAGGCAGTTGGGTAATTAA
          1 CATACATTCAGTCCTGAAATTAGAGTTATGTTTCACATTT-AGGCAGTTGGGTAATTAA

                                                                    
      18373 CATACATTCAGTCCTGAAATTAGAGTTATGTTTCACATTTAGGCAGTTGGGTAATT
          1 CATACATTCAGTCCTGAAATTAGAGTTATGTTTCACATTTAGGCAGTTGGGTAATT

      18429 GATTGCAGGG


Statistics
Matches: 56,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  58   16  0.29
  59   40  0.71

ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37


Consensus pattern (58 bp):   
CATACATTCAGTCCTGAAATTAGAGTTATGTTTCACATTTAGGCAGTTGGGTAATTAA

Found at i:21654 original size:53 final size:51

Alignment explanation


    Indices: 21565--21669  Score: 176
    Period size: 53  Copynumber: 2.0  Consensus size: 51

      21555 TTTAACTGAC

                                                               
      21565 ATCTGTACATGAACATCATTCTCGTTTTCAGTGATTATTACCACCTGAAGA
          1 ATCTGTACATGAACATCATTCTCGTTTTCAGTGATTATTACCACCTGAAGA

                                                                  
      21616 ATCTGTAC-TGAACATCATTCTCAATGTTTTCAGTGATTATTACCACCTGAAGA
          1 ATCTGTACATGAACATCATTCTC---GTTTTCAGTGATTATTACCACCTGAAGA

             
      21669 A
          1 A

      21670 GCAAATCGAG


Statistics
Matches: 51,  Mismatches: 0, Indels: 4
        0.93            0.00        0.07

Matches are distributed among these distances:
  50   14  0.27
  51    8  0.16
  53   29  0.57

ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35


Consensus pattern (51 bp):   
ATCTGTACATGAACATCATTCTCGTTTTCAGTGATTATTACCACCTGAAGA

Found at i:36561 original size:2 final size:2

Alignment explanation


    Indices: 36556--36580  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      36546 ATATATATAT

                                                 
      36556 AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG A

      36581 AACGTTATCA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00


Consensus pattern (2 bp):   
AG

Done.