Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000575.1 Kokia drynarioides strain JFW-HI SEQ_111498, 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: 2350
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37


Found at i:462 original size:18 final size:20

Alignment explanation


    Indices: 439--476  Score: 53
    Period size: 19  Copynumber: 2.0  Consensus size: 20

        429 ATGTGGCAAT

                                
        439 CCAAC-TAGATTTT-AAATG
          1 CCAACTTAGATTTTCAAATG

                   *            
        457 CCAACTTGGATTTTCAAATG
          1 CCAACTTAGATTTTCAAATG

        477 GAATGAGAAT


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

Matches are distributed among these distances:
  18    5  0.29
  19    7  0.41
  20    5  0.29

ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34


Consensus pattern (20 bp):   
CCAACTTAGATTTTCAAATG

Found at i:516 original size:18 final size:16

Alignment explanation


    Indices: 484--527  Score: 56
    Period size: 14  Copynumber: 2.8  Consensus size: 16

        474 ATGGAATGAG

                            
        484 AATAAATTTTTAATTA
          1 AATAAATTTTTAATTA

                            
        500 AATAAA--TTTAATTA
          1 AATAAATTTTTAATTA

             *            
        514 ATTAAAATTTTTAA
          1 AAT-AAATTTTTAA

        528 ATCCTAAACC


Statistics
Matches: 24,  Mismatches: 1, Indels: 5
        0.80            0.03        0.17

Matches are distributed among these distances:
  14   10  0.42
  15    3  0.12
  16    6  0.25
  17    5  0.21

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


Consensus pattern (16 bp):   
AATAAATTTTTAATTA

Found at i:743 original size:18 final size:18

Alignment explanation


    Indices: 722--758  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        712 TTAGTTTTCG

                       *      
        722 AATTCGAATAACTCGAAT
          1 AATTCGAATAAATCGAAT

                *             
        740 AATTTGAATAAATCGAAT
          1 AATTCGAATAAATCGAAT

             
        758 A
          1 A

        759 TTAAACTATA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30


Consensus pattern (18 bp):   
AATTCGAATAAATCGAAT

Found at i:825 original size:20 final size:20

Alignment explanation


    Indices: 793--831  Score: 62
    Period size: 19  Copynumber: 1.9  Consensus size: 20

        783 TACCTCAAAC

                                 
        793 CCCAAACATTTTTATTTTTCT
          1 CCCAAACATTTTT-TTTTTCT

                               
        814 CCCAAA-ATTTTTTTTTTC
          1 CCCAAACATTTTTTTTTTC

        832 CCACTTTCCC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  19    6  0.33
  20    6  0.33
  21    6  0.33

ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54


Consensus pattern (20 bp):   
CCCAAACATTTTTTTTTTCT

Found at i:1018 original size:30 final size:29

Alignment explanation


    Indices: 975--1032  Score: 91
    Period size: 30  Copynumber: 2.0  Consensus size: 29

        965 ATTTTTTATT

                                         
        975 TTTCCTCAAAACTTTTAC-TCCCTCTCAC
          1 TTTCCTCAAAACTTTTACTTCCCTCTCAC

                                          
       1003 TTTCCTCTTAAAACTTTTACTTCCCTCTCA
          1 TTTCCTC--AAAACTTTTACTTCCCTCTCA

       1033 TCTCCCCCCC


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  28    7  0.26
  30   11  0.41
  31    9  0.33

ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43


Consensus pattern (29 bp):   
TTTCCTCAAAACTTTTACTTCCCTCTCAC

Done.