Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008256.1 Kokia drynarioides strain JFW-HI SEQ_122921, 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: 10069
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33


Found at i:1786 original size:52 final size:52

Alignment explanation


    Indices: 1697--1828  Score: 176
    Period size: 52  Copynumber: 2.5  Consensus size: 52

       1687 GATCTTCGAA

                            *   * *          *        *          
       1697 TCATATACTCACGATGGCACTTTGTCATT-AGACCTCATAATTCGTAAAGGAT
          1 TCATATACTCACGATGACACATAGTCATTGA-AACTCATAATCCGTAAAGGAT

                *              *                                
       1749 TCATTTACTCACGATGACATATAGTCATTGAAACTCATAATCCGTAAAGGAT
          1 TCATATACTCACGATGACACATAGTCATTGAAACTCATAATCCGTAAAGGAT

                                *       
       1801 TCATATACTCACGATGACACGTAGTCAT
          1 TCATATACTCACGATGACACATAGTCAT

       1829 CGGACCTCTT


Statistics
Matches: 69,  Mismatches: 10, Indels: 2
        0.85            0.12        0.02

Matches are distributed among these distances:
  52   68  0.99
  53    1  0.01

ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31


Consensus pattern (52 bp):   
TCATATACTCACGATGACACATAGTCATTGAAACTCATAATCCGTAAAGGAT

Found at i:2170 original size:13 final size:13

Alignment explanation


    Indices: 2152--2176  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2142 TACAATTTTA

                         
       2152 CAAAATAACCATG
          1 CAAAATAACCATG

                        
       2165 CAAAATAACCAT
          1 CAAAATAACCAT

       2177 TCTCTTACAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.24, G:0.04, T:0.16


Consensus pattern (13 bp):   
CAAAATAACCATG

Found at i:2691 original size:21 final size:21

Alignment explanation


    Indices: 2663--2710  Score: 62
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       2653 ACTTTCATCA

                     *           
       2663 TTAACCTTACTTAATCA-CTC
          1 TTAACCTTAATTAATCATCTC

                                   
       2683 TTAATCCTTAATTAATCATTCTC
          1 TTAA-CCTTAATTAATCA-TCTC

                 
       2706 TTAAC
          1 TTAAC

       2711 ACCTAAATGT


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  20    4  0.17
  21   12  0.50
  22    1  0.04
  23    7  0.29

ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44


Consensus pattern (21 bp):   
TTAACCTTAATTAATCATCTC
Done.