Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011084.1 Kokia drynarioides strain JFW-HI SEQ_126057, 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: 7247
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33


Found at i:3286 original size:12 final size:12

Alignment explanation


    Indices: 3274--3316  Score: 50
    Period size: 12  Copynumber: 3.6  Consensus size: 12

       3264 TCCATAACCT

                       *
       3274 CGTCCTCGTCCT
          1 CGTCCTCGTCCA

                 *      
       3286 CGTCCGCGTCCA
          1 CGTCCTCGTCCA

                 *      
       3298 CGTCCACGTCCA
          1 CGTCCTCGTCCA

              *    
       3310 CGGCCTC
          1 CGTCCTC

       3317 TACCTCTTTG


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  12   26  1.00

ACGTcount: A:0.07, C:0.51, G:0.21, T:0.21


Consensus pattern (12 bp):   
CGTCCTCGTCCA

Found at i:3295 original size:18 final size:18

Alignment explanation


    Indices: 3274--3308  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3264 TCCATAACCT

                 *     *      
       3274 CGTCCTCGTCCTCGTCCG
          1 CGTCCACGTCCACGTCCG

                             
       3292 CGTCCACGTCCACGTCC
          1 CGTCCACGTCCACGTCC

       3309 ACGGCCTCTA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.06, C:0.51, G:0.20, T:0.23


Consensus pattern (18 bp):   
CGTCCACGTCCACGTCCG

Found at i:5695 original size:21 final size:22

Alignment explanation


    Indices: 5678--5737  Score: 61
    Period size: 21  Copynumber: 2.8  Consensus size: 22

       5668 AAATTTTCTC

                       *          
       5678 CGGTTTAAATGGTTTTTTCACT
          1 CGGTTTAAATGATTTTTTCACT

                    *         *   
       5700 CGGTTTAACTGA-TTTTTAACT
          1 CGGTTTAAATGATTTTTTCACT

             *                
       5721 CAGTTT-AATCGATTTTT
          1 CGGTTTAAAT-GATTTTT

       5738 AATCTGTTAA


Statistics
Matches: 31,  Mismatches: 5, Indels: 4
        0.77            0.12        0.10

Matches are distributed among these distances:
  20    2  0.06
  21   15  0.48
  22   14  0.45

ACGTcount: A:0.22, C:0.13, G:0.15, T:0.50


Consensus pattern (22 bp):   
CGGTTTAAATGATTTTTTCACT

Found at i:5738 original size:21 final size:21

Alignment explanation


    Indices: 5691--5739  Score: 64
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5681 TTTAAATGGT

                 *    *          
       5691 TTTTTCACTCGGTTTAACTGA
          1 TTTTTAACTCAGTTTAACTGA

                                  
       5712 TTTTTAACTCAGTTTAA-TCGA
          1 TTTTTAACTCAGTTTAACT-GA

                   
       5733 TTTTTAA
          1 TTTTTAA

       5740 TCTGTTAAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  20    1  0.04
  21   24  0.96

ACGTcount: A:0.24, C:0.14, G:0.10, T:0.51


Consensus pattern (21 bp):   
TTTTTAACTCAGTTTAACTGA

Found at i:5899 original size:3 final size:3

Alignment explanation


    Indices: 5891--5918  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       5881 AAAAAATATA

                                                 
       5891 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T

       5919 TACCTCAAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TAT

Done.