Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008628.1 Kokia drynarioides strain JFW-HI SEQ_123307, 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: 3877
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34


Found at i:14 original size:9 final size:9

Alignment explanation


    Indices: 1--44  Score: 56
    Period size: 9  Copynumber: 5.0  Consensus size: 9

                     
          1 TTATAAAAA
          1 TTATAAAAA

                      
         10 TTATAATAAA
          1 TTATAA-AAA

              *      
         20 TTTTAAAAA
          1 TTATAAAAA

                     
         29 --ATAAAAA
          1 TTATAAAAA

                     
         36 TTATAAAAA
          1 TTATAAAAA

         45 ATCATTTAAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 6
        0.79            0.05        0.16

Matches are distributed among these distances:
   7    6  0.20
   9   16  0.53
  10    8  0.27

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (9 bp):   
TTATAAAAA

Found at i:312 original size:30 final size:30

Alignment explanation


    Indices: 273--372  Score: 98
    Period size: 30  Copynumber: 3.3  Consensus size: 30

        263 TTATTATACT

                *                          
        273 TTAATATTTTA-ATATTTTTAAAAGATTAAA
          1 TTAAAATTTTATA-ATTTTTAAAAGATTAAA

                        *            *    
        303 TTAAAATTTTATCATTTTTAAAA-AATAAA
          1 TTAAAATTTTATAATTTTTAAAAGATTAAA

            *      *                   *   
        332 ATAAAATATTATAATTTTT-AAAGCATCAAA
          1 TTAAAATTTTATAATTTTTAAAAG-ATTAAA

                       
        362 TATAAAATTTT
          1 T-TAAAATTTT

        373 CTAAAAGGCC


Statistics
Matches: 56,  Mismatches: 10, Indels: 7
        0.77            0.14        0.10

Matches are distributed among these distances:
  28    3  0.05
  29   21  0.38
  30   24  0.43
  31    8  0.14

ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45


Consensus pattern (30 bp):   
TTAAAATTTTATAATTTTTAAAAGATTAAA

Found at i:336 original size:29 final size:28

Alignment explanation


    Indices: 278--372  Score: 91
    Period size: 29  Copynumber: 3.2  Consensus size: 28

        268 ATACTTTAAT

                                *    *    
        278 ATTTTAATATTTTTAAAAGATTAAATTAAA
          1 ATTTT-ATATTTTTAAAA-AATAAAATAAA

                                         
        308 ATTTTATCATTTTTAAAAAATAAAATAAA
          1 ATTTTAT-ATTTTTAAAAAATAAAATAAA

              *              **            
        337 ATATTATAATTTTTAAAGCATCAAATATAAA
          1 ATTTTAT-ATTTTTAAAAAAT-AAA-ATAAA

                 
        368 ATTTT
          1 ATTTT

        373 CTAAAAGGCC


Statistics
Matches: 55,  Mismatches: 7, Indels: 5
        0.82            0.10        0.07

Matches are distributed among these distances:
  29   28  0.51
  30   18  0.33
  31    9  0.16

ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44


Consensus pattern (28 bp):   
ATTTTATATTTTTAAAAAATAAAATAAA

Found at i:882 original size:35 final size:34

Alignment explanation


    Indices: 842--907  Score: 91
    Period size: 33  Copynumber: 1.9  Consensus size: 34

        832 TCATAATTGT

                                                 
        842 TTTTAATTTAATTTATACTTATAT-AAT-TTTTTGAA
          1 TTTTAA-TT-ATTTATA-TTATATGAATATTTTTGAA

                                           
        877 TTTTAATTATTTATATTATATGAATATTTTT
          1 TTTTAATTATTTATATTATATGAATATTTTT

        908 TTGAATATAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
  32    6  0.21
  33   10  0.34
  34    7  0.24
  35    6  0.21

ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62


Consensus pattern (34 bp):   
TTTTAATTATTTATATTATATGAATATTTTTGAA

Found at i:908 original size:35 final size:36

Alignment explanation


    Indices: 842--913  Score: 89
    Period size: 36  Copynumber: 2.0  Consensus size: 36

        832 TCATAATTGT

                                                
        842 TTTTAATTTAATTTATACTTATATAA-TTTTTTGAA
          1 TTTTAATTTAATTTATACTTATATAATTTTTTTGAA

                                                   
        877 TTTTAA-TT-ATTTATA-TTATATGAATATTTTTTTGAA
          1 TTTTAATTTAATTTATACTTATAT--A-ATTTTTTTGAA

             
        913 T
          1 T

        914 ATATTTGTGT


Statistics
Matches: 33,  Mismatches: 0, Indels: 7
        0.82            0.00        0.17

Matches are distributed among these distances:
  32    6  0.18
  33    7  0.21
  34    3  0.09
  35    7  0.21
  36   10  0.30

ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61


Consensus pattern (36 bp):   
TTTTAATTTAATTTATACTTATATAATTTTTTTGAA
Done.