Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008104.1 Kokia drynarioides strain JFW-HI SEQ_122762, 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: 5672
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33


Found at i:597 original size:66 final size:66

Alignment explanation


    Indices: 487--623  Score: 165
    Period size: 66  Copynumber: 2.1  Consensus size: 66

        477 GGGGAAATAA

                                          *                                  
        487 GGAGAGAGTTAGCTTTACGCTTCACTTTTGGGACATGCTTGACTCTATAAGTC-T-TTTGGTGTG
          1 GGAGAGAGTTAGCTTTACGCTTCACTTTTGAGACATGCTTGACTC--TAAGTCATATTTGGTGTG

               
        550 TTT
         64 TTT

                  *           *               *             *                
        553 GGAGAGTGTTAG-TTATATGCTTCACTTTTGAGATATG-TTCGACTCTGAGTCATATTTGGTGTG
          1 GGAGAGAGTTAGCTT-TACGCTTCACTTTTGAGACATGCTT-GACTCTAAGTCATATTTGGTGTG

               
        616 TTT
         64 TTT

                 
        619 GGAGA
          1 GGAGA

        624 TTCGCATATT


Statistics
Matches: 62,  Mismatches: 5, Indels: 8
        0.83            0.07        0.11

Matches are distributed among these distances:
  64    5  0.08
  65    5  0.08
  66   52  0.84

ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41


Consensus pattern (66 bp):   
GGAGAGAGTTAGCTTTACGCTTCACTTTTGAGACATGCTTGACTCTAAGTCATATTTGGTGTGTT
T

Found at i:733 original size:23 final size:23

Alignment explanation


    Indices: 700--897  Score: 263
    Period size: 23  Copynumber: 8.6  Consensus size: 23

        690 ATTAAATGTG

                           *       
        700 TTAAATATTAATGTGTTTTATGC
          1 TTAAATATTAATGTGATTTATGC

                  *     *          
        723 TTAAATGTTAATATGATTTATGC
          1 TTAAATATTAATGTGATTTATGC

                   *                
        746 TTACAA-GTTAATGTGATTTATGC
          1 TTA-AATATTAATGTGATTTATGC

                               *   
        769 TTAAATATTAATGTGATTTGTGC
          1 TTAAATATTAATGTGATTTATGC

                          *        
        792 TTAAATATTAATGTAATTTATGC
          1 TTAAATATTAATGTGATTTATGC

                  *     *         *
        815 TTAAATGTTAATATGATTTATGT
          1 TTAAATATTAATGTGATTTATGC

               *                   
        838 TTACATATTAATGTGATTTATGC
          1 TTAAATATTAATGTGATTTATGC

                        * *    *   
        861 TTAAATATTAATCTAATTTGTGC
          1 TTAAATATTAATGTGATTTATGC

                          
        884 TTAAATATTAATGT
          1 TTAAATATTAATGT

        898 TAAAACGTAT


Statistics
Matches: 152,  Mismatches: 21, Indels: 4
        0.86            0.12        0.02

Matches are distributed among these distances:
  22    2  0.01
  23  148  0.97
  24    2  0.01

ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48


Consensus pattern (23 bp):   
TTAAATATTAATGTGATTTATGC

Found at i:3428 original size:18 final size:18

Alignment explanation


    Indices: 3405--3440  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       3395 GTCCTTATAT

                              
       3405 GCCTCAAAATGCTTTAAG
          1 GCCTCAAAATGCTTTAAG

                              
       3423 GCCTCAAAATGCTTTAAG
          1 GCCTCAAAATGCTTTAAG

       3441 ATTCACCTCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28


Consensus pattern (18 bp):   
GCCTCAAAATGCTTTAAG

Found at i:4194 original size:15 final size:15

Alignment explanation


    Indices: 4174--4203  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       4164 AATTTCATGC

                           
       4174 TTCAATCACCATGTT
          1 TTCAATCACCATGTT

                           
       4189 TTCAATCACCATGTT
          1 TTCAATCACCATGTT

       4204 ATCACTTAGC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40


Consensus pattern (15 bp):   
TTCAATCACCATGTT
Done.