Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003338.1 Kokia drynarioides strain JFW-HI SEQ_116040, 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: 4767
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:777 original size:21 final size:21

Alignment explanation


    Indices: 751--792  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        741 CATCTACGTG

                                 
        751 GCAAGTTAACTGGCCACATCA
          1 GCAAGTTAACTGGCCACATCA

                       *         
        772 GCAAGTTAACTTGCCACATCA
          1 GCAAGTTAACTGGCCACATCA

        793 TCATTCCTGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21


Consensus pattern (21 bp):   
GCAAGTTAACTGGCCACATCA

Found at i:896 original size:30 final size:31

Alignment explanation


    Indices: 829--897  Score: 88
    Period size: 31  Copynumber: 2.3  Consensus size: 31

        819 AATGTTAATC

                 *      *         *        
        829 AGTGAATGTTTTTTCACTTTTTGATAACGTT
          1 AGTGACTGTTTTGTCACTTTTTCATAACGTT

                                           
        860 AGTGACTGTTTTGTCACTTTTTCA-AA-GTT
          1 AGTGACTGTTTTGTCACTTTTTCATAACGTT

                     
        889 GAGTGACTG
          1 -AGTGACTG

        898 AAATGAAATC


Statistics
Matches: 34,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  29    3  0.09
  30   10  0.29
  31   21  0.62

ACGTcount: A:0.22, C:0.12, G:0.20, T:0.46


Consensus pattern (31 bp):   
AGTGACTGTTTTGTCACTTTTTCATAACGTT

Found at i:2478 original size:60 final size:61

Alignment explanation


    Indices: 2403--2522  Score: 206
    Period size: 60  Copynumber: 2.0  Consensus size: 61

       2393 AAATAAAATC

                      *                     *                            
       2403 CTAATGACATTGTTATAAGGTTGTTTGTT-AACAAAGGAAATTATTTTAAAGAGCTTTCTT
          1 CTAATGACATCGTTATAAGGTTGTTTGTTAAAAAAAGGAAATTATTTTAAAGAGCTTTCTT

                                                *                       
       2463 CTAATGACATCGTTATAAGGTTGTTTGTTAAAAAAATGAAATTATTTTAAAGAGCTTTCT
          1 CTAATGACATCGTTATAAGGTTGTTTGTTAAAAAAAGGAAATTATTTTAAAGAGCTTTCT

       2523 CCTAGATATC


Statistics
Matches: 56,  Mismatches: 3, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  60   28  0.50
  61   28  0.50

ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41


Consensus pattern (61 bp):   
CTAATGACATCGTTATAAGGTTGTTTGTTAAAAAAAGGAAATTATTTTAAAGAGCTTTCTT

Found at i:3818 original size:50 final size:50

Alignment explanation


    Indices: 3725--3819  Score: 136
    Period size: 50  Copynumber: 1.9  Consensus size: 50

       3715 GCTTGAACAC

                           *            * *      **           
       3725 GGGCTTGTGTCAAGGTCGTGTGTCATTATACTAGGTTGTAGGAGGTACAT
          1 GGGCTTGTGTCAAGGCCGTGTGTCATTAAAATAGGTTACAGGAGGTACAT

                       *                                 
       3775 GGGCTTGTGTCCAGGCCGTGTGTCATTAAAATAGGTTACAGGAGG
          1 GGGCTTGTGTCAAGGCCGTGTGTCATTAAAATAGGTTACAGGAGG

       3820 CACACGATCC


Statistics
Matches: 39,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  50   39  1.00

ACGTcount: A:0.21, C:0.14, G:0.35, T:0.31


Consensus pattern (50 bp):   
GGGCTTGTGTCAAGGCCGTGTGTCATTAAAATAGGTTACAGGAGGTACAT
Done.