Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009747.1 Kokia drynarioides strain JFW-HI SEQ_124466, 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: 7181
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37


Found at i:705 original size:41 final size:41

Alignment explanation


    Indices: 639--775  Score: 193
    Period size: 41  Copynumber: 3.3  Consensus size: 41

        629 ACTTGACGTA

                          *     *                     
        639 TAAATGGAAGACTCATGTCTTGAGATGAGCATGAGATTATAT
          1 TAAA-GGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT

                                             *       
        681 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGATATTATAT
          1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT

                 *          *    *      *            
        722 TAAAGCAAGACTCGTGACTCGGGATGAGAATGAGATTATAT
          1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT

                         
        763 TCAAAGGAAGACT
          1 T-AAAGGAAGACT

        776 TATGACTCGG


Statistics
Matches: 85,  Mismatches: 9, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  41   71  0.84
  42   14  0.16

ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27


Consensus pattern (41 bp):   
TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT

Found at i:799 original size:41 final size:40

Alignment explanation


    Indices: 639--799  Score: 171
    Period size: 41  Copynumber: 3.9  Consensus size: 40

        629 ACTTGACGTA

                          *  *  *                     
        639 TAAATGGAAGACTCATGTCTTGAGATGAGCATGAGATTATAT
          1 TAAA-GGAAGACTCGTGACTCG-GATGAGCATGAGATTATAT

                            *                *       
        681 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGATATTATAT
          1 TAAAGGAAGACTCGTGACTCG-GATGAGCATGAGATTATAT

                 *                      *            
        722 TAAAGCAAGACTCGTGACTCGGGATGAGAATGAGATTATAT
          1 TAAAGGAAGACTCGTGACTC-GGATGAGCATGAGATTATAT

                         **                 *     
        763 TCAAAGGAAGACTTATGACTCGG-TAGAGCATAAGATT
          1 T-AAAGGAAGACTCGTGACTCGGAT-GAGCATGAGATT

        800 GTTTAAAAGG


Statistics
Matches: 104,  Mismatches: 12, Indels: 7
        0.85            0.10        0.06

Matches are distributed among these distances:
  40    1  0.01
  41   82  0.79
  42   21  0.20

ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27


Consensus pattern (40 bp):   
TAAAGGAAGACTCGTGACTCGGATGAGCATGAGATTATAT

Found at i:1748 original size:5 final size:5

Alignment explanation


    Indices: 1738--1784  Score: 60
    Period size: 5  Copynumber: 9.4  Consensus size: 5

       1728 ATGTTGTGTA

                                         *                   *       
       1738 AATAT AATAT AATA- AATAT AATTAA AATAT AATAT AATAT GATAT AA
          1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT AATAT AA

       1785 ACAAATAATG


Statistics
Matches: 36,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
   4    4  0.11
   5   28  0.78
   6    4  0.11

ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36


Consensus pattern (5 bp):   
AATAT

Found at i:1846 original size:27 final size:28

Alignment explanation


    Indices: 1801--1874  Score: 69
    Period size: 27  Copynumber: 2.6  Consensus size: 28

       1791 AATGCAAACA

                  *    *  *            *
       1801 TAATATTATATGAAGTATA-ATGGAAAT
          1 TAATATAATATAAATTATATATGGAAAG

                                * *     
       1828 TAATATAATATAAATTATATTTTGAAAG
          1 TAATATAATATAAATTATATATGGAAAG

            *                  
       1856 GAATATAATATAAAATTAT
          1 TAATATAATAT-AAATTAT

       1875 GAGCTTACAA


Statistics
Matches: 38,  Mismatches: 7, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  27   16  0.42
  28   15  0.39
  29    7  0.18

ACGTcount: A:0.51, C:0.00, G:0.09, T:0.39


Consensus pattern (28 bp):   
TAATATAATATAAATTATATATGGAAAG

Found at i:3885 original size:17 final size:18

Alignment explanation


    Indices: 3863--3896  Score: 61
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       3853 ATAACAATTA

                              
       3863 TGAAGATTTTGG-ATATG
          1 TGAAGATTTTGGCATATG

                             
       3880 TGAAGATTTTGGCATAT
          1 TGAAGATTTTGGCATAT

       3897 TCCTCGAAGC


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17   12  0.75
  18    4  0.25

ACGTcount: A:0.29, C:0.03, G:0.26, T:0.41


Consensus pattern (18 bp):   
TGAAGATTTTGGCATATG
Done.