Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006208.1 Kokia drynarioides strain JFW-HI SEQ_120779, 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: 4270
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:811 original size:29 final size:29

Alignment explanation


    Indices: 769--832  Score: 119
    Period size: 29  Copynumber: 2.2  Consensus size: 29

        759 CAATAATATT

                 *                       
        769 ATCATGATATTTCATAGAAAATGCAAAGG
          1 ATCATAATATTTCATAGAAAATGCAAAGG

                                         
        798 ATCATAATATTTCATAGAAAATGCAAAGG
          1 ATCATAATATTTCATAGAAAATGCAAAGG

                  
        827 ATCATA
          1 ATCATA

        833 TATAAATTAG


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   34  1.00

ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28


Consensus pattern (29 bp):   
ATCATAATATTTCATAGAAAATGCAAAGG

Found at i:844 original size:28 final size:28

Alignment explanation


    Indices: 782--844  Score: 83
    Period size: 29  Copynumber: 2.2  Consensus size: 28

        772 ATGATATTTC

                                     ** 
        782 ATAGAAAATGCAAAGGATCATAATATTT
          1 ATAGAAAATGCAAAGGATCATAATAAAT

                                          
        810 CATAGAAAATGCAAAGGATCATATATAAAT
          1 -ATAGAAAATGCAAAGGATCATA-ATAAAT

                  
        840 -TAGAA
          1 ATAGAA

        845 CCATGTCTTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  28    5  0.16
  29   22  0.71
  30    4  0.13

ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25


Consensus pattern (28 bp):   
ATAGAAAATGCAAAGGATCATAATAAAT

Found at i:2878 original size:15 final size:14

Alignment explanation


    Indices: 2858--2887  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       2848 TTTGTTCTTT

                           
       2858 TTTTTTATATTATTA
          1 TTTTTTATATT-TTA

                          
       2873 TTTTTTATATTTTA
          1 TTTTTTATATTTTA

             
       2887 T
          1 T

       2888 AAGTATGTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    4  0.27
  15   11  0.73

ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77


Consensus pattern (14 bp):   
TTTTTTATATTTTA

Found at i:3300 original size:18 final size:18

Alignment explanation


    Indices: 3273--3311  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       3263 GAAGGGTGCT

                 *            
       3273 TCGGGTAGAGGAAACGTC
          1 TCGGGCAGAGGAAACGTC

                       *  *   
       3291 TCGGGCAGAGGGAATGTC
          1 TCGGGCAGAGGAAACGTC

               
       3309 TCG
          1 TCG

       3312 AGAGTCGAAG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.23, C:0.18, G:0.41, T:0.18


Consensus pattern (18 bp):   
TCGGGCAGAGGAAACGTC
Done.