Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004238.1 Kokia drynarioides strain JFW-HI SEQ_117504, 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: 23860
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:332 original size:23 final size:23

Alignment explanation


    Indices: 306--349  Score: 88
    Period size: 23  Copynumber: 1.9  Consensus size: 23

        296 AGTAAAGATT

                                   
        306 ATTACTGCATAACTCATAAAATC
          1 ATTACTGCATAACTCATAAAATC

                                 
        329 ATTACTGCATAACTCATAAAA
          1 ATTACTGCATAACTCATAAAA

        350 CTAAAGATTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30


Consensus pattern (23 bp):   
ATTACTGCATAACTCATAAAATC

Found at i:363 original size:30 final size:29

Alignment explanation


    Indices: 291--364  Score: 79
    Period size: 23  Copynumber: 2.7  Consensus size: 29

        281 GTATGATTTA

                                          
        291 ATAAAAGTAAAGATTATTACTGCATAACTC
          1 ATAAAA-TAAAGATTATTACTGCATAACTC

                         *               
        321 -----ATAAA-ATCATTACTGCATAACTC
          1 ATAAAATAAAGATTATTACTGCATAACTC

                                 
        344 ATAAAACTAAAGATTATTACT
          1 ATAAAA-TAAAGATTATTACT

        365 TCCATCACAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 14
        0.69            0.04        0.27

Matches are distributed among these distances:
  23   17  0.49
  24    4  0.11
  25    1  0.03
  28    1  0.03
  29    4  0.11
  30    8  0.23

ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31


Consensus pattern (29 bp):   
ATAAAATAAAGATTATTACTGCATAACTC

Found at i:5783 original size:18 final size:18

Alignment explanation


    Indices: 5760--5797  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       5750 TTTTCGACAT

                     *     *  
       5760 CGGCACCGGTACCGATGC
          1 CGGCACCGGAACCGACGC

                              
       5778 CGGCACCGGAACCGACGC
          1 CGGCACCGGAACCGACGC

              
       5796 CG
          1 CG

       5798 ATGAGATTTC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.18, C:0.42, G:0.34, T:0.05


Consensus pattern (18 bp):   
CGGCACCGGAACCGACGC

Found at i:15291 original size:7 final size:7

Alignment explanation


    Indices: 15279--15306  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

      15269 CAAAAAGAAG

                   
      15279 GGTAACC
          1 GGTAACC

                   
      15286 GGTAACC
          1 GGTAACC

                   
      15293 GGTAACC
          1 GGTAACC

                   
      15300 GGTAACC
          1 GGTAACC

      15307 AGATTAGATC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14


Consensus pattern (7 bp):   
GGTAACC

Found at i:19998 original size:15 final size:16

Alignment explanation


    Indices: 19978--20008  Score: 55
    Period size: 15  Copynumber: 2.0  Consensus size: 16

      19968 TAAAAATAAC

                            
      19978 AAAATTAA-TAAAAAT
          1 AAAATTAATTAAAAAT

                            
      19993 AAAATTAATTAAAAAT
          1 AAAATTAATTAAAAAT

      20009 TAACACTATT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    8  0.53
  16    7  0.47

ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29


Consensus pattern (16 bp):   
AAAATTAATTAAAAAT

Done.