Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007242.1 Kokia drynarioides strain JFW-HI SEQ_121857, 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: 17452
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:566 original size:36 final size:37

Alignment explanation


    Indices: 515--602  Score: 88
    Period size: 36  Copynumber: 2.4  Consensus size: 37

        505 TATGGTAAAA

                   *                             
        515 AAAAAATGATATTATAAATTCTAAAAAATTATATTAT
          1 AAAAAATAATATTATAAATTCTAAAAAATTATATTAT

                            *   *  *   *      * *
        552 AAAAAATAAT-TTATATATTTTATAAAGTTATATAAC
          1 AAAAAATAATATTATAAATTCTAAAAAATTATATTAT

               *   *       
        588 AAACAATTATATTAT
          1 AAAAAATAATATTAT

        603 TTAAGTCCTA


Statistics
Matches: 41,  Mismatches: 9, Indels: 2
        0.79            0.17        0.04

Matches are distributed among these distances:
  36   28  0.68
  37   13  0.32

ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40


Consensus pattern (37 bp):   
AAAAAATAATATTATAAATTCTAAAAAATTATATTAT

Found at i:925 original size:16 final size:15

Alignment explanation


    Indices: 890--934  Score: 58
    Period size: 14  Copynumber: 3.1  Consensus size: 15

        880 ATTGAACAAT

                     *     
        890 TTATAAAACCTTAT-
          1 TTATAAAACTTTATA

                            
        904 TTATAAAACTTGTATA
          1 TTATAAAACTT-TATA

                           
        920 TTAT-AAACTTTATA
          1 TTATAAAACTTTATA

             
        934 T
          1 T

        935 ATATTTTTTA


Statistics
Matches: 28,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  14   15  0.54
  15    9  0.32
  16    4  0.14

ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47


Consensus pattern (15 bp):   
TTATAAAACTTTATA

Found at i:3371 original size:30 final size:29

Alignment explanation


    Indices: 3335--3394  Score: 84
    Period size: 30  Copynumber: 2.0  Consensus size: 29

       3325 GTAACCTTGA

                    * *      *            
       3335 TATAATGTTATCTTGTGTGAGCAACTCTAT
          1 TATAATGTCAGCTTGTGCGAGCAACT-TAT

                                         
       3365 TATAATGTCAGCTTGTGCGAGCAACTTAT
          1 TATAATGTCAGCTTGTGCGAGCAACTTAT

             
       3394 T
          1 T

       3395 CTCGTGTATC


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  29    4  0.15
  30   23  0.85

ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40


Consensus pattern (29 bp):   
TATAATGTCAGCTTGTGCGAGCAACTTAT

Found at i:13322 original size:17 final size:18

Alignment explanation


    Indices: 13278--13323  Score: 51
    Period size: 17  Copynumber: 2.7  Consensus size: 18

      13268 CATATCCGCC

                   *          
      13278 AGACAATTCTATTCATCA
          1 AGACAATACTATTCATCA

                  *          *
      13296 AGA-AAAACTATTCA-CT
          1 AGACAATACTATTCATCA

                        
      13312 AGACAATACTAT
          1 AGACAATACTAT

      13324 CTGCCAAGCG


Statistics
Matches: 23,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  16    4  0.17
  17   16  0.70
  18    3  0.13

ACGTcount: A:0.46, C:0.20, G:0.07, T:0.28


Consensus pattern (18 bp):   
AGACAATACTATTCATCA

Found at i:17116 original size:19 final size:19

Alignment explanation


    Indices: 17080--17117  Score: 51
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      17070 GACTACAAAA

                               
      17080 TTCATATATCCTTGTATTT
          1 TTCATATATCCTTGTATTT

                      *         
      17099 TTCACTATATGCTT-TATTT
          1 TTCA-TATATCCTTGTATTT

      17118 ATCAATATTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    9  0.53
  20    8  0.47

ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58


Consensus pattern (19 bp):   
TTCATATATCCTTGTATTT
Done.