Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009994.1 Kokia drynarioides strain JFW-HI SEQ_124749, 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: 7177
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:422 original size:85 final size:84

Alignment explanation


    Indices: 277--444  Score: 318
    Period size: 85  Copynumber: 2.0  Consensus size: 84

        267 CTCGTCCGGA

                                                                             
        277 TGGTACTGCTGGCTGGGGAAATTCGTCGCGCCTGGGTGGTTACGTTGGCGAGTTTCCAACGTCTT
          1 TGGTACTGCTGGCTGGGGAAATTCGTCGCGCCTGGGTGGTTACGTTGGCGAGTTTCCAACGTCTT

                               
        342 TTTCGCCATATGTTCCTCT
         66 TTTCGCCATATGTTCCTCT

                                                               *             
        361 TGNGTACTGCTGGCTGGGGAAATTCGTCGCGCCTGGGTGGTTACGTTGGCGGGTTTCCAACGTCT
          1 TG-GTACTGCTGGCTGGGGAAATTCGTCGCGCCTGGGTGGTTACGTTGGCGAGTTTCCAACGTCT

                               
        426 TTTTCGCCATATGTTCCTC
         65 TTTTCGCCATATGTTCCTC

        445 CTGGCCGTCG


Statistics
Matches: 82,  Mismatches: 1, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
  84    2  0.02
  85   80  0.98

ACGTcount: A:0.11, C:0.24, G:0.30, T:0.34


Consensus pattern (84 bp):   
TGGTACTGCTGGCTGGGGAAATTCGTCGCGCCTGGGTGGTTACGTTGGCGAGTTTCCAACGTCTT
TTTCGCCATATGTTCCTCT

Found at i:4884 original size:2 final size:2

Alignment explanation


    Indices: 4877--4902  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       4867 GCGGCCTGAA

                                                  
       4877 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       4903 TTTTAAAAGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:5095 original size:15 final size:16

Alignment explanation


    Indices: 5069--5098  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       5059 TGACTCTTAA

                            
       5069 AATTTAAATTTTTTGC
          1 AATTTAAATTTTTTGC

                           
       5085 AATTT-AATTTTTTG
          1 AATTTAAATTTTTTG

       5099 TAGATATACT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    9  0.64
  16    5  0.36

ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60


Consensus pattern (16 bp):   
AATTTAAATTTTTTGC

Found at i:5335 original size:35 final size:36

Alignment explanation


    Indices: 5284--5352  Score: 104
    Period size: 35  Copynumber: 1.9  Consensus size: 36

       5274 TTGTGTGTTG

                       *             *          
       5284 CCTAAAGAGAGGACACG-AGGACTTTACCCAACTTA
          1 CCTAAAGAGAGAACACGAAGGACTTCACCCAACTTA

                                        *     
       5319 CCTAAAGAGAGAACACGAAGGACTTCACTCAACT
          1 CCTAAAGAGAGAACACGAAGGACTTCACCCAACT

       5353 CGCCTTGTCT


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  35   16  0.53
  36   14  0.47

ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16


Consensus pattern (36 bp):   
CCTAAAGAGAGAACACGAAGGACTTCACCCAACTTA

Done.