Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003141.1 Kokia drynarioides strain JFW-HI SEQ_115723, 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: 20643
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:4514 original size:22 final size:21

Alignment explanation


    Indices: 4474--4514  Score: 55
    Period size: 22  Copynumber: 1.9  Consensus size: 21

       4464 TAAAAAAAAA

                          *      
       4474 TAATTATTTAATATGATCACT
          1 TAATTATTTAATATAATCACT

                         *      
       4495 TAATTATTTTAATTTAATCA
          1 TAATTA-TTTAATATAATCA

       4515 GTTTTTCTTA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    6  0.35
  22   11  0.65

ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51


Consensus pattern (21 bp):   
TAATTATTTAATATAATCACT

Found at i:6588 original size:7 final size:7

Alignment explanation


    Indices: 6576--6603  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

       6566 GCTTTATATT

                   
       6576 AAGATTC
          1 AAGATTC

                   
       6583 AAGATTC
          1 AAGATTC

                   
       6590 AAGATTC
          1 AAGATTC

                   
       6597 AAGATTC
          1 AAGATTC

       6604 GGAGTTGTGT


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

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29


Consensus pattern (7 bp):   
AAGATTC

Found at i:8926 original size:18 final size:18

Alignment explanation


    Indices: 8905--8939  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       8895 CCTATATCGA

                    *         
       8905 TCCCTATCCCGATCACGT
          1 TCCCTATCACGATCACGT

                             
       8923 TCCCTATCACGATCACG
          1 TCCCTATCACGATCACG

       8940 GTCACGATCT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.20, C:0.43, G:0.11, T:0.26


Consensus pattern (18 bp):   
TCCCTATCACGATCACGT

Found at i:11635 original size:17 final size:17

Alignment explanation


    Indices: 11580--11640  Score: 54
    Period size: 17  Copynumber: 3.5  Consensus size: 17

      11570 AAAAAATAAA

                               
      11580 AATATTTGTTATAATTTTT
          1 AATATTT-TT-TAATTTTT

                *            * 
      11599 -AT-GTTTTTAATCATTAT
          1 AATATTTTTTAAT--TTTT

                             
      11616 AATATTTTTTAATTTTT
          1 AATATTTTTTAATTTTT

                    
      11633 AATATTTT
          1 AATATTTT

      11641 AATTAATTTC


Statistics
Matches: 34,  Mismatches: 4, Indels: 10
        0.71            0.08        0.21

Matches are distributed among these distances:
  15    4  0.12
  16    2  0.06
  17   16  0.47
  18    4  0.12
  19    8  0.24

ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64


Consensus pattern (17 bp):   
AATATTTTTTAATTTTT
Done.