Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013488.1 Kokia drynarioides strain JFW-HI SEQ_128514, 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: 10852
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34


Found at i:2517 original size:18 final size:18

Alignment explanation


    Indices: 2491--2531  Score: 64
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       2481 TTAATAATGC

                *           * 
       2491 TTTTATCTCAAAAGTGTT
          1 TTTTGTCTCAAAAGTGCT

                              
       2509 TTTTGTCTCAAAAGTGCT
          1 TTTTGTCTCAAAAGTGCT

                 
       2527 TTTTG
          1 TTTTG

       2532 AGAAACAATG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51


Consensus pattern (18 bp):   
TTTTGTCTCAAAAGTGCT

Found at i:2796 original size:20 final size:19

Alignment explanation


    Indices: 2763--2806  Score: 72
    Period size: 20  Copynumber: 2.3  Consensus size: 19

       2753 TTTCTTTGTT

                               
       2763 AAAAT-TTTATTTATATTA
          1 AAAATATTTATTTATATTA

                                
       2781 AAAATATTTATGTTATATTA
          1 AAAATATTTAT-TTATATTA

                  
       2801 AAAATA
          1 AAAATA

       2807 AAAGGTAAAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  18    5  0.21
  19    5  0.21
  20   14  0.58

ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48


Consensus pattern (19 bp):   
AAAATATTTATTTATATTA

Found at i:2803 original size:19 final size:17

Alignment explanation


    Indices: 2761--2803  Score: 59
    Period size: 19  Copynumber: 2.4  Consensus size: 17

       2751 TTTTTCTTTG

                             
       2761 TTAAAATTTTATTTATA
          1 TTAAAATTTTATTTATA

                                
       2778 TTAAAAATATTTATGTTATA
          1 TT-AAAAT-TTTAT-TTATA

                  
       2798 TTAAAA
          1 TTAAAA

       2804 ATAAAAGGTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  17    2  0.09
  18    5  0.22
  19    9  0.39
  20    7  0.30

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51


Consensus pattern (17 bp):   
TTAAAATTTTATTTATA

Found at i:4634 original size:18 final size:17

Alignment explanation


    Indices: 4611--4646  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       4601 TTTTTTTAAC

                              
       4611 TTTTAAAAATAATAAAAA
          1 TTTT-AAAATAATAAAAA

                   *         
       4629 TTTTAAATTAATAAAAA
          1 TTTTAAAATAATAAAAA

             
       4646 T
          1 T

       4647 AAAATTATAC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17   13  0.76
  18    4  0.24

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (17 bp):   
TTTTAAAATAATAAAAA

Found at i:4710 original size:30 final size:32

Alignment explanation


    Indices: 4647--4717  Score: 85
    Period size: 30  Copynumber: 2.3  Consensus size: 32

       4637 TAATAAAAAT

                     *                      
       4647 AAAATTATACTTTAATTCTCTTAAAAATGATA
          1 AAAATTATAATTTAATTCTCTTAAAAATGATA

                               *      * *   
       4679 AAAATT-TAATTTAA-TCTTTTAAAATTTATA
          1 AAAATTATAATTTAATTCTCTTAAAAATGATA

                      
       4709 AAAA-TATAA
          1 AAAATTATAA

       4718 AAAATTTAAT


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
  29    1  0.03
  30   20  0.59
  31    7  0.21
  32    6  0.18

ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42


Consensus pattern (32 bp):   
AAAATTATAATTTAATTCTCTTAAAAATGATA

Found at i:6630 original size:18 final size:18

Alignment explanation


    Indices: 6592--6630  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       6582 TTAATAATGC

                           ** 
       6592 TTTTATCTCAAAAGTGTT
          1 TTTTATCTCAAAAGTACT

                *             
       6610 TTTTGTCTCAAAAGTACT
          1 TTTTATCTCAAAAGTACT

               
       6628 TTT
          1 TTT

       6631 GAAAAGCAAT


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:0.26, C:0.13, G:0.10, T:0.51


Consensus pattern (18 bp):   
TTTTATCTCAAAAGTACT

Found at i:8634 original size:21 final size:24

Alignment explanation


    Indices: 8610--8657  Score: 57
    Period size: 22  Copynumber: 2.1  Consensus size: 24

       8600 CCTAACGAAG

                      *             
       8610 GTGG-CATCGTGATACC-C-AGAA
          1 GTGGACATCGCGATACCTCAAGAA

                 *                  
       8631 GTGGATATCGCGATACCTCAAGAA
          1 GTGGACATCGCGATACCTCAAGAA

               
       8655 GTG
          1 GTG

       8658 TCGAGCCTTG


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  21    4  0.18
  22   10  0.45
  23    1  0.05
  24    7  0.32

ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21


Consensus pattern (24 bp):   
GTGGACATCGCGATACCTCAAGAA
Done.