Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003310.1 Kokia drynarioides strain JFW-HI SEQ_115996, 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: 13688
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38


Found at i:1978 original size:12 final size:12

Alignment explanation


    Indices: 1953--1989  Score: 56
    Period size: 12  Copynumber: 3.1  Consensus size: 12

       1943 TGTTGTTCAA

                   *    
       1953 TTCCTCTTCCTC
          1 TTCCTCTCCCTC

               *        
       1965 TTCTTCTCCCTC
          1 TTCCTCTCCCTC

                        
       1977 TTCCTCTCCCTC
          1 TTCCTCTCCCTC

             
       1989 T
          1 T

       1990 CCTGCTGTTT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  12   22  1.00

ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49


Consensus pattern (12 bp):   
TTCCTCTCCCTC

Found at i:1990 original size:18 final size:18

Alignment explanation


    Indices: 1955--1991  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       1945 TTGTTCAATT

                       * *    
       1955 CCTCTTCCTCTTCTTCTC
          1 CCTCTTCCTCTCCCTCTC

                              
       1973 CCTCTTCCTCTCCCTCTC
          1 CCTCTTCCTCTCCCTCTC

             
       1991 C
          1 C

       1992 TGCTGTTTCT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43


Consensus pattern (18 bp):   
CCTCTTCCTCTCCCTCTC

Found at i:4903 original size:2 final size:2

Alignment explanation


    Indices: 4896--4938  Score: 77
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       4886 CTCCTTTCAT

                                                    *                     
       4896 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

             
       4938 T
          1 T

       4939 TTACCACACA


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   39  1.00

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


Consensus pattern (2 bp):   
TC

Found at i:13528 original size:9 final size:9

Alignment explanation


    Indices: 13514--13538  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

      13504 TTCAGACTCA

                     
      13514 GATTCTTCT
          1 GATTCTTCT

                     
      13523 GATTCTTCT
          1 GATTCTTCT

                   
      13532 GATTCTT
          1 GATTCTT

      13539 TCTCAAAACT


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

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.12, C:0.20, G:0.12, T:0.56


Consensus pattern (9 bp):   
GATTCTTCT
Done.