Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003808.1 Kokia drynarioides strain JFW-HI SEQ_116803, 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: 12821
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33


Found at i:1991 original size:23 final size:25

Alignment explanation


    Indices: 1965--2011  Score: 62
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       1955 TACTAAATCC

                           *         
       1965 ATTTATTT-ATT-ATTTATATAGTT
          1 ATTTATTTCATTCATATATATAGTT

                *                   
       1988 ATTTTTTTCATTCATATATATAGT
          1 ATTTATTTCATTCATATATATAGT

       2012 GGACCCGCCC


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  23    7  0.35
  24    3  0.15
  25   10  0.50

ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62


Consensus pattern (25 bp):   
ATTTATTTCATTCATATATATAGTT

Found at i:2604 original size:24 final size:24

Alignment explanation


    Indices: 2572--2619  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2562 ATATTATAAG

                                    
       2572 TATATAAATAATCAACACTACCAC
          1 TATATAAATAATCAACACTACCAC

                                    
       2596 TATATAAATAATCAACACTACCAC
          1 TATATAAATAATCAACACTACCAC

       2620 AAAGAGCTAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25


Consensus pattern (24 bp):   
TATATAAATAATCAACACTACCAC

Found at i:6715 original size:14 final size:13

Alignment explanation


    Indices: 6690--6723  Score: 52
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       6680 TTCAAGGTTT

                         
       6690 AAGTTTAGATTTG
          1 AAGTTTAGATTTG

                          
       6703 AAGTTTGAGATTTG
          1 AAGTTT-AGATTTG

                    
       6717 -AGTTTAG
          1 AAGTTTAG

       6724 GGTTTAGGAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  12    2  0.10
  13   11  0.55
  14    7  0.35

ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44


Consensus pattern (13 bp):   
AAGTTTAGATTTG

Found at i:7964 original size:2 final size:2

Alignment explanation


    Indices: 7952--7983  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       7942 ATACTTAATC

                  *                                        
       7952 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       7984 GTATGTATGT


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:9761 original size:6 final size:6

Alignment explanation


    Indices: 9750--9779  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       9740 AAAAGGGGTT

                                              
       9750 GGGATG GGGATG GGGATG GGGATG GGGATG
          1 GGGATG GGGATG GGGATG GGGATG GGGATG

       9780 AGGTTTAAGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.17, C:0.00, G:0.67, T:0.17


Consensus pattern (6 bp):   
GGGATG

Done.