Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002399.1 Kokia drynarioides strain JFW-HI SEQ_114485, 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: 3380
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38


Found at i:504 original size:2 final size:2

Alignment explanation


    Indices: 497--527  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

        487 TTTTAAAAAT

                                                          
        497 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        528 TAGAATTTTG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:574 original size:19 final size:20

Alignment explanation


    Indices: 550--588  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        540 TTTTTTTAAA

                                
        550 TATAAA-TTTTAAAATTTTT
          1 TATAAATTTTTAAAATTTTT

                                
        569 TATAAATTTTTAAAATTTTT
          1 TATAAATTTTTAAAATTTTT

        589 GAAATATTAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19    6  0.32
  20   13  0.68

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (20 bp):   
TATAAATTTTTAAAATTTTT

Found at i:1975 original size:19 final size:17

Alignment explanation


    Indices: 1951--1989  Score: 51
    Period size: 19  Copynumber: 2.2  Consensus size: 17

       1941 CTCAGTTCAA

                               
       1951 AATCATCCCTTCATTCATC
          1 AATCATCCC-TCATTC-TC

                   *         
       1970 AATCATCTCTCATTCTC
          1 AATCATCCCTCATTCTC

               
       1987 AAT
          1 AAT

       1990 TCTTTTTGCA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  17    5  0.26
  18    6  0.32
  19    8  0.42

ACGTcount: A:0.28, C:0.33, G:0.00, T:0.38


Consensus pattern (17 bp):   
AATCATCCCTCATTCTC

Found at i:2851 original size:23 final size:23

Alignment explanation


    Indices: 2818--2861  Score: 72
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       2808 TTTATTCACG

                                    
       2818 TTTTGAGGGTTTATTATTTTTCGA
          1 TTTTGAGGGTTTATT-TTTTTCGA

                                 
       2842 TTTTG-GGGTTTATTTTTTTC
          1 TTTTGAGGGTTTATTTTTTTC

       2862 TCCATCTTTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  22    6  0.30
  23    9  0.45
  24    5  0.25

ACGTcount: A:0.11, C:0.05, G:0.20, T:0.64


Consensus pattern (23 bp):   
TTTTGAGGGTTTATTTTTTTCGA

Found at i:3108 original size:28 final size:28

Alignment explanation


    Indices: 3076--3131  Score: 112
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       3066 GATAAATACT

                                        
       3076 TAATTGAATTGAAACTCGATTGGTTGAA
          1 TAATTGAATTGAAACTCGATTGGTTGAA

                                        
       3104 TAATTGAATTGAAACTCGATTGGTTGAA
          1 TAATTGAATTGAAACTCGATTGGTTGAA

       3132 GGGAAATATT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   28  1.00

ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36


Consensus pattern (28 bp):   
TAATTGAATTGAAACTCGATTGGTTGAA
Done.