Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000896.1 Kokia drynarioides strain JFW-HI SEQ_112023, 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: 7955
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31


Found at i:2245 original size:23 final size:23

Alignment explanation


    Indices: 2219--2272  Score: 72
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       2209 CGTGGCAGCT

                  *                
       2219 AGTCAGTAGCTTCTAGAAAGTCC
          1 AGTCAGCAGCTTCTAGAAAGTCC

                        *     *   *
       2242 AGTCAGCAGCTTTTAGAAGGTCT
          1 AGTCAGCAGCTTCTAGAAAGTCC

                    
       2265 AGTCAGCA
          1 AGTCAGCA

       2273 AGGATGGACG


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  23   27  1.00

ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26


Consensus pattern (23 bp):   
AGTCAGCAGCTTCTAGAAAGTCC

Found at i:4714 original size:36 final size:32

Alignment explanation


    Indices: 4687--4753  Score: 88
    Period size: 30  Copynumber: 2.2  Consensus size: 32

       4677 GAAAAATTCC

                                             
       4687 AGAATAAAACTGAGGTTCATCTACAAG--AATT
          1 AGAA-AAAACTGAGGTTCATCTACAAGAAAATT

                  *                         
       4718 AGAAAAGACTGAGGTTCATCTACAAG--AATT
          1 AGAAAAAACTGAGGTTCATCTACAAGAAAATT

                  
       4748 AGAAAA
          1 AGAAAA

       4754 GCAAATGAGC


Statistics
Matches: 35,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  30   31  0.89
  31    4  0.11

ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22


Consensus pattern (32 bp):   
AGAAAAAACTGAGGTTCATCTACAAGAAAATT

Found at i:4729 original size:30 final size:30

Alignment explanation


    Indices: 4695--4754  Score: 120
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       4685 CCAGAATAAA

                                          
       4695 ACTGAGGTTCATCTACAAGAATTAGAAAAG
          1 ACTGAGGTTCATCTACAAGAATTAGAAAAG

                                          
       4725 ACTGAGGTTCATCTACAAGAATTAGAAAAG
          1 ACTGAGGTTCATCTACAAGAATTAGAAAAG

       4755 CAAATGAGCC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   30  1.00

ACGTcount: A:0.43, C:0.13, G:0.20, T:0.23


Consensus pattern (30 bp):   
ACTGAGGTTCATCTACAAGAATTAGAAAAG

Found at i:6598 original size:21 final size:21

Alignment explanation


    Indices: 6572--6613  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6562 ACAGGAGTAC

                                 
       6572 GGTTTAAAGTTAATGGACAAA
          1 GGTTTAAAGTTAATGGACAAA

                                 
       6593 GGTTTAAAGTTAATGGACAAA
          1 GGTTTAAAGTTAATGGACAAA

       6614 AGTTGAAAAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.43, C:0.05, G:0.24, T:0.29


Consensus pattern (21 bp):   
GGTTTAAAGTTAATGGACAAA

Found at i:6798 original size:25 final size:25

Alignment explanation


    Indices: 6752--6799  Score: 62
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       6742 TCTTTTATTA

                             *       
       6752 ATTTATTTTAATTATTTTTATTTCT
          1 ATTTATTTTAATTATTTGTATTTCT

                     *              
       6777 ATTTATTTTTATT-TTTGGTATTT
          1 ATTTATTTTAATTATTT-GTATTT

       6800 TAAATTTTTA


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

Matches are distributed among these distances:
  24    3  0.15
  25   17  0.85

ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73


Consensus pattern (25 bp):   
ATTTATTTTAATTATTTGTATTTCT

Found at i:7772 original size:13 final size:13

Alignment explanation


    Indices: 7754--7782  Score: 58
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       7744 TACGAACAGC

                         
       7754 AAAAAAAAAAGCA
          1 AAAAAAAAAAGCA

                         
       7767 AAAAAAAAAAGCA
          1 AAAAAAAAAAGCA

               
       7780 AAA
          1 AAA

       7783 GGTTTAAAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00


Consensus pattern (13 bp):   
AAAAAAAAAAGCA
Done.