Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001353.1 Kokia drynarioides strain JFW-HI SEQ_112802, 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: 6773
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35


Found at i:711 original size:16 final size:15

Alignment explanation


    Indices: 668--723  Score: 60
    Period size: 16  Copynumber: 3.7  Consensus size: 15

        658 TTATTTAAAT

                          *
        668 TAAAATT-AAAATTT
          1 TAAAATTAAAAATTA

                            
        682 TAAAATTAAAAAATTA
          1 TAAAATT-AAAAATTA

                          * 
        698 TAATAATTAAAAATAA
          1 TAA-AATTAAAAATTA

             *        
        714 TTAAATTAAA
          1 TAAAATTAAA

        724 GTATGATGCC


Statistics
Matches: 36,  Mismatches: 3, Indels: 5
        0.82            0.07        0.11

Matches are distributed among these distances:
  14    7  0.19
  15    7  0.19
  16   18  0.50
  17    4  0.11

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


Consensus pattern (15 bp):   
TAAAATTAAAAATTA

Found at i:878 original size:2 final size:2

Alignment explanation


    Indices: 871--902  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

        861 TGTAAAATTA

                                                 *         
        871 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        903 TTACAGTTAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:3978 original size:18 final size:18

Alignment explanation


    Indices: 3951--3988  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       3941 TCCTACGTGG

                              
       3951 CAGTCCAACTAG-ATTTT
          1 CAGTCCAACTAGAATTTT

                       *       
       3968 CAGTGCCAACTTGAATTTT
          1 CAGT-CCAACTAGAATTTT

              
       3987 CA
          1 CA

       3989 AATGGGATGA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  17    4  0.22
  18    7  0.39
  19    7  0.39

ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34


Consensus pattern (18 bp):   
CAGTCCAACTAGAATTTT
Done.