Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001591.1 Kokia drynarioides strain JFW-HI SEQ_113205, 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: 38202
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:508 original size:22 final size:23

Alignment explanation


    Indices: 463--514  Score: 79
    Period size: 23  Copynumber: 2.3  Consensus size: 23

        453 GAAACAATAA

                                   
        463 GCACACACAATGCAATCCAGTAG
          1 GCACACACAATGCAATCCAGTAG

                     *             
        486 GCACACACAGTGCAAT-CAGTAG
          1 GCACACACAATGCAATCCAGTAG

              *    
        508 GCGCACA
          1 GCACACA

        515 TAGCGCAAAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  22   12  0.44
  23   15  0.56

ACGTcount: A:0.37, C:0.31, G:0.21, T:0.12


Consensus pattern (23 bp):   
GCACACACAATGCAATCCAGTAG

Found at i:522 original size:22 final size:23

Alignment explanation


    Indices: 463--522  Score: 68
    Period size: 22  Copynumber: 2.7  Consensus size: 23

        453 GAAACAATAA

                     **            
        463 GCACACACAATGCAATCCAGTAG
          1 GCACACACAGCGCAATCCAGTAG

                      *            
        486 GCACACACAGTGCAAT-CAGTAG
          1 GCACACACAGCGCAATCCAGTAG

              *    *       
        508 GCGCACATAGCGCAA
          1 GCACACACAGCGCAA

        523 ATCAATTAGT


Statistics
Matches: 33,  Mismatches: 4, Indels: 1
        0.87            0.11        0.03

Matches are distributed among these distances:
  22   18  0.55
  23   15  0.45

ACGTcount: A:0.37, C:0.30, G:0.22, T:0.12


Consensus pattern (23 bp):   
GCACACACAGCGCAATCCAGTAG

Found at i:3922 original size:12 final size:12

Alignment explanation


    Indices: 3905--3957  Score: 51
    Period size: 12  Copynumber: 4.5  Consensus size: 12

       3895 ATTTAAGATA

                        
       3905 TTATTTAT-TAT
          1 TTATTTATGTAT

                         
       3916 TTAATTT-TGTAT
          1 TT-ATTTATGTAT

                          
       3928 TTATTTATGTTTAT
          1 TTATTTATG--TAT

                        
       3942 TT-TTT-TGTAT
          1 TTATTTATGTAT

                  
       3952 TTATTT
          1 TTATTT

       3958 TTTAGAGTTT


Statistics
Matches: 36,  Mismatches: 0, Indels: 12
        0.75            0.00        0.25

Matches are distributed among these distances:
  10    5  0.14
  11   10  0.28
  12   13  0.36
  13    3  0.08
  14    5  0.14

ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74


Consensus pattern (12 bp):   
TTATTTATGTAT

Found at i:6926 original size:16 final size:15

Alignment explanation


    Indices: 6885--6931  Score: 51
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       6875 TTATGTTTAT

                           
       6885 ATTTTTATTTTGATC
          1 ATTTTTATTTTGATC

                **           
       6900 A-TTCAACTTTTCGATC
          1 ATTTTTA-TTTT-GATC

                           
       6916 ATTTTTATTTTGATC
          1 ATTTTTATTTTGATC

             
       6931 A
          1 A

       6932 CCTAAAAACT


Statistics
Matches: 25,  Mismatches: 4, Indels: 6
        0.71            0.11        0.17

Matches are distributed among these distances:
  14    3  0.12
  15   10  0.40
  16    9  0.36
  17    3  0.12

ACGTcount: A:0.23, C:0.13, G:0.06, T:0.57


Consensus pattern (15 bp):   
ATTTTTATTTTGATC

Found at i:32549 original size:3 final size:3

Alignment explanation


    Indices: 32541--32565  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

      32531 AATTAAGCCC

                                             
      32541 TGA TGA TGA TGA TGA TGA TGA TGA T
          1 TGA TGA TGA TGA TGA TGA TGA TGA T

      32566 CTCACTGTTG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36


Consensus pattern (3 bp):   
TGA

Done.