Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009345.1 Kokia drynarioides strain JFW-HI SEQ_124052, 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: 2749
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33


Found at i:348 original size:39 final size:39

Alignment explanation


    Indices: 294--370  Score: 154
    Period size: 39  Copynumber: 2.0  Consensus size: 39

        284 TTAGTTATAC

                                                   
        294 TCTTTTGGTATATATCGCAAAAGCCACTGATCTTCTTGT
          1 TCTTTTGGTATATATCGCAAAAGCCACTGATCTTCTTGT

                                                  
        333 TCTTTTGGTATATATCGCAAAAGCCACTGATCTTCTTG
          1 TCTTTTGGTATATATCGCAAAAGCCACTGATCTTCTTG

        371 GGATAATATG


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  39   38  1.00

ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40


Consensus pattern (39 bp):   
TCTTTTGGTATATATCGCAAAAGCCACTGATCTTCTTGT

Found at i:2269 original size:19 final size:19

Alignment explanation


    Indices: 2247--2284  Score: 51
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       2237 TTACTAATGT

                                
       2247 AACTA-ATATATATTTCAAA
          1 AACTACATATAT-TTTCAAA

                    *          
       2266 AACTACATTTATTTTCAAA
          1 AACTACATATATTTTCAAA

       2285 TATTACATGT


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

Matches are distributed among these distances:
  19   12  0.71
  20    5  0.29

ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39


Consensus pattern (19 bp):   
AACTACATATATTTTCAAA

Found at i:2718 original size:17 final size:17

Alignment explanation


    Indices: 2658--2721  Score: 57
    Period size: 17  Copynumber: 4.1  Consensus size: 17

       2648 CAAATGATTT

                             
       2658 TAAAATTATTAAAATTA
          1 TAAAATTATTAAAATTA

                   *         
       2675 T----TTTTTAAAA-TA
          1 TAAAATTATTAAAATTA

                *  *  *      
       2687 TAAATTTTTTTAAATTA
          1 TAAAATTATTAAAATTA

                             
       2704 TAAAATTATTAAAATTA
          1 TAAAATTATTAAAATTA

             
       2721 T
          1 T

       2722 TTTTTTGAAA


Statistics
Matches: 37,  Mismatches: 5, Indels: 10
        0.71            0.10        0.19

Matches are distributed among these distances:
  12    3  0.08
  13    8  0.22
  16    8  0.22
  17   18  0.49

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


Consensus pattern (17 bp):   
TAAAATTATTAAAATTA

Found at i:2724 original size:30 final size:31

Alignment explanation


    Indices: 2690--2747  Score: 100
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       2680 TAAAATATAA

                         *                 
       2690 ATTTTTTT-AAATTATAAAATTATTAAAATT
          1 ATTTTTTTGAAATAATAAAATTATTAAAATT

                                        
       2720 ATTTTTTTGAAATAATAAAATTATTAAA
          1 ATTTTTTTGAAATAATAAAATTATTAAA

       2748 TA


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  30    8  0.31
  31   18  0.69

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


Consensus pattern (31 bp):   
ATTTTTTTGAAATAATAAAATTATTAAAATT

Done.