Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004582.1 Kokia drynarioides strain JFW-HI SEQ_118070, 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: 5539
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33


Found at i:588 original size:25 final size:26

Alignment explanation


    Indices: 560--618  Score: 70
    Period size: 25  Copynumber: 2.3  Consensus size: 26

        550 GTGGTAACAA

                              *        
        560 ATTTCTAATTT-CTAA-TTTTTAATTT
          1 ATTT-TAATTTACTAACTCTTTAATTT

                       *              
        585 A-TTTAATTTATTAACTCTTTAATTT
          1 ATTTTAATTTACTAACTCTTTAATTT

                     
        610 ATTTTAATT
          1 ATTTTAATT

        619 GTTAATATTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 5
        0.81            0.06        0.14

Matches are distributed among these distances:
  23    6  0.21
  24    5  0.17
  25   11  0.38
  26    7  0.24

ACGTcount: A:0.31, C:0.07, G:0.00, T:0.63


Consensus pattern (26 bp):   
ATTTTAATTTACTAACTCTTTAATTT

Found at i:2839 original size:13 final size:12

Alignment explanation


    Indices: 2821--2850  Score: 51
    Period size: 13  Copynumber: 2.4  Consensus size: 12

       2811 TGCTCAAGAA

                         
       2821 AAAAAGAAAAATG
          1 AAAAAGAAAAA-G

                        
       2834 AAAAAGAAAAAG
          1 AAAAAGAAAAAG

                 
       2846 AAAAA
          1 AAAAA

       2851 TATAGAGCAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12    6  0.35
  13   11  0.65

ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03


Consensus pattern (12 bp):   
AAAAAGAAAAAG

Found at i:2843 original size:5 final size:6

Alignment explanation


    Indices: 2821--2850  Score: 51
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       2811 TGCTCAAGAA

                                              
       2821 AAAAAG AAAAATG AAAAAG AAAAAG AAAAA
          1 AAAAAG AAAAA-G AAAAAG AAAAAG AAAAA

       2851 TATAGAGCAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   6   17  0.74
   7    6  0.26

ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03


Consensus pattern (6 bp):   
AAAAAG

Found at i:5452 original size:22 final size:20

Alignment explanation


    Indices: 5427--5479  Score: 61
    Period size: 22  Copynumber: 2.5  Consensus size: 20

       5417 TTTACTTTCT

                                  
       5427 TTTTCTTTTTCTGCTTTAATGG
          1 TTTTCTTTTT-TGCTTT-ATGG

                               * 
       5449 TTTTCTATTTTTGCTTTATTG
          1 TTTTCT-TTTTTGCTTTATGG

                      
       5470 TTTTGCTTTT
          1 TTTT-CTTTT

       5480 AATTTTAGTT


Statistics
Matches: 28,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  21   10  0.36
  22   14  0.50
  23    4  0.14

ACGTcount: A:0.08, C:0.11, G:0.11, T:0.70


Consensus pattern (20 bp):   
TTTTCTTTTTTGCTTTATGG
Done.