Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007132.1 Kokia drynarioides strain JFW-HI SEQ_121744, whole genome shotgun sequence

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: 16803
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:3919 original size:2 final size:2

Alignment explanation


    Indices: 3914--3949  Score: 58
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       3904 TGTCCCCCCC

                                                                    
       3914 CT CT CT CT CT CT CT CT CT CT CT -T CT CT CT -T CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

       3950 TCTGCTTCTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   30  0.94

ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53


Consensus pattern (2 bp):   
CT

Found at i:3933 original size:14 final size:14

Alignment explanation


    Indices: 3914--3949  Score: 58
    Period size: 13  Copynumber: 2.7  Consensus size: 14

       3904 TGTCCCCCCC

                          
       3914 CTCTCTCTCTCTCT
          1 CTCTCTCTCTCTCT

                          
       3928 CTCTCTCT-TCTCT
          1 CTCTCTCTCTCTCT

                      
       3941 CT-TCTCTCT
          1 CTCTCTCTCT

       3950 TCTGCTTCTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  12    5  0.24
  13    8  0.38
  14    8  0.38

ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53


Consensus pattern (14 bp):   
CTCTCTCTCTCTCT

Found at i:3950 original size:14 final size:15

Alignment explanation


    Indices: 3914--3952  Score: 64
    Period size: 14  Copynumber: 2.7  Consensus size: 15

       3904 TGTCCCCCCC

                           
       3914 CTCTCTC-TCTCTCT
          1 CTCTCTCTTCTCTCT

                           
       3928 CTCTCTCTTCTCTCT
          1 CTCTCTCTTCTCTCT

                       
       3943 -TCTCTCTTCT
          1 CTCTCTCTTCT

       3953 GCTTCTTCAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  14   17  0.71
  15    7  0.29

ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54


Consensus pattern (15 bp):   
CTCTCTCTTCTCTCT

Found at i:8394 original size:15 final size:14

Alignment explanation


    Indices: 8364--8391  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       8354 TTGTATTTTT

                          
       8364 TTTTTTTTAAATAA
          1 TTTTTTTTAAATAA

                          
       8378 TTTTTTTTAAATAA
          1 TTTTTTTTAAATAA

       8392 ATTACTTCTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (14 bp):   
TTTTTTTTAAATAA

Found at i:12867 original size:2 final size:2

Alignment explanation


    Indices: 12855--12890  Score: 58
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      12845 AAGAAGCAGA

                                                                    
      12855 AG AG AG A- AG AG AG A- AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

      12891 GGGGGGGACA


Statistics
Matches: 32,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   30  0.94

ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:12890 original size:14 final size:14

Alignment explanation


    Indices: 12855--12890  Score: 58
    Period size: 13  Copynumber: 2.7  Consensus size: 14

      12845 AAGAAGCAGA

                          
      12855 AGAGAGA-AGAGAG
          1 AGAGAGAGAGAGAG

                          
      12868 A-AGAGAGAGAGAG
          1 AGAGAGAGAGAGAG

                      
      12881 AGAGAGAGAG
          1 AGAGAGAGAG

      12891 GGGGGGGACA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  12    5  0.24
  13    8  0.38
  14    8  0.38

ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00


Consensus pattern (14 bp):   
AGAGAGAGAGAGAG
Done.