Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013153.1 Kokia drynarioides strain JFW-HI SEQ_128172, 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: 13507
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:2632 original size:36 final size:35

Alignment explanation


    Indices: 2585--2655  Score: 124
    Period size: 36  Copynumber: 2.0  Consensus size: 35

       2575 TTCGTGCTGA

                                       *       
       2585 TCTCGGGCCTCGGTACGCGGTCCGTGATATTCTCC
          1 TCTCGGGCCTCGGTACGCGGTCCGTGACATTCTCC

                                                
       2620 NTCTCGGGCCTCGGTACGCGGTCCGTGACATTCTCC
          1 -TCTCGGGCCTCGGTACGCGGTCCGTGACATTCTCC

       2656 CCTACTGAAT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  36   34  1.00

ACGTcount: A:0.08, C:0.35, G:0.28, T:0.27


Consensus pattern (35 bp):   
TCTCGGGCCTCGGTACGCGGTCCGTGACATTCTCC

Found at i:4654 original size:14 final size:14

Alignment explanation


    Indices: 4635--4664  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       4625 GGTCAAGGGT

                          
       4635 GTGGCTATTTTGGA
          1 GTGGCTATTTTGGA

                          
       4649 GTGGCTATTTTGGA
          1 GTGGCTATTTTGGA

              
       4663 GT
          1 GT

       4665 AGCCTTTGAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.13, C:0.07, G:0.37, T:0.43


Consensus pattern (14 bp):   
GTGGCTATTTTGGA

Found at i:5988 original size:101 final size:100

Alignment explanation


    Indices: 5813--6018  Score: 394
    Period size: 101  Copynumber: 2.0  Consensus size: 100

       5803 CCTTCTCAAC

                                       *                                     
       5813 ACGAAGGTCAAGTCTCTTGGCAGCCCGTTCGGACACGAATAATTTTGAGGCACCTATGTCCACTA
          1 ACGAAGGTCAAGTCTCTTGGCAGCCCGCTCGGACACGAATAATTTTGAGGCACCTATGTCCACTA

                                               
       5878 GTGCGCTCAACTTTTGGCCTGCCACAGTGATGTCT
         66 GTGCGCTCAACTTTTGGCCTGCCACAGTGATGTCT

                                                                             
       5913 NACGAAGGTCAAGTCTCTTGGCAGCCCGCTCGGACACGAATAATTTTGAGGCACCTATGTCCACT
          1 -ACGAAGGTCAAGTCTCTTGGCAGCCCGCTCGGACACGAATAATTTTGAGGCACCTATGTCCACT

                                                
       5978 AGTGCGCTCAACTTTTGGCCTGCCACAGTGATGTCT
         65 AGTGCGCTCAACTTTTGGCCTGCCACAGTGATGTCT

                 
       6014 ACGAA
          1 ACGAA

       6019 CATCAGTCCC


Statistics
Matches: 104,  Mismatches: 1, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
 100    5  0.05
 101   99  0.95

ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26


Consensus pattern (100 bp):   
ACGAAGGTCAAGTCTCTTGGCAGCCCGCTCGGACACGAATAATTTTGAGGCACCTATGTCCACTA
GTGCGCTCAACTTTTGGCCTGCCACAGTGATGTCT

Found at i:8108 original size:18 final size:18

Alignment explanation


    Indices: 8085--8121  Score: 65
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       8075 TTTGTAATGA

                         *    
       8085 TTTTATCTCAAAAGTGCT
          1 TTTTATCTCAAAAATGCT

                              
       8103 TTTTATCTCAAAAATGCT
          1 TTTTATCTCAAAAATGCT

             
       8121 T
          1 T

       8122 CTGAAAAGTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46


Consensus pattern (18 bp):   
TTTTATCTCAAAAATGCT
Done.