Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001581.1 Kokia drynarioides strain JFW-HI SEQ_113189, 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: 2691
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35


Found at i:172 original size:96 final size:96

Alignment explanation


    Indices: 3--177  Score: 223
    Period size: 96  Copynumber: 1.8  Consensus size: 96

          1 TC

                          ** *                   *                       *   
          3 TCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCAGAATCGAAGATAAGGAA
          1 TCGATTTGAAGAAAAATAGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGAAGATAAAGAA

               *                           
         68 ATATTGCCTCGATTAAGAGTATTCAATTATT
         66 ATACTGCCTCGATTAAGAGTATTCAATTATT

                     *                                                       
         99 TCGATTTGAGGAAAAATAGCACCTAGTAAGTTAAGGCACAA-ATTTTC-GAAACTCGAA-ATAAA
          1 TCGATTTGAAGAAAAATAGCACCTAGTAAGTTAAGGCACAATA-TTTCAG-AA-TCGAAGATAAA

                              
        161 -AGAATACTGCCTCGATT
         63 GA-AATACTGCCTCGATT

        178 TTAAAGTTTT


Statistics
Matches: 68,  Mismatches: 7, Indels: 8
        0.82            0.08        0.10

Matches are distributed among these distances:
  95    3  0.04
  96   60  0.88
  97    5  0.07

ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28


Consensus pattern (96 bp):   
TCGATTTGAAGAAAAATAGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGAAGATAAAGAA
ATACTGCCTCGATTAAGAGTATTCAATTATT

Found at i:455 original size:30 final size:29

Alignment explanation


    Indices: 432--670  Score: 266
    Period size: 30  Copynumber: 8.1  Consensus size: 29

        422 TTTTATGAAA

                *                         
        432 TTTTAGGGTCAAAAATGGGATTTTTGGAAG
          1 TTTTGGGGT-AAAAATGGGATTTTTGGAAG

              **                  *      
        462 TTCGGGGGTAAAAATGGGATTTATGGAAG
          1 TTTTGGGGTAAAAATGGGATTTTTGGAAG

                                          
        491 TTTTGGGGTTAAAAATGGGATTTTTGGAAG
          1 TTTTGGGG-TAAAAATGGGATTTTTGGAAG

                             **      *    
        521 TTTTGGGGTTAAAAATGAAATTTTTAGAAG
          1 TTTTGGGG-TAAAAATGGGATTTTTGGAAG

               *             *            
        551 TTTGGGGGTAAAAATGGAATTTTTTGGAAG
          1 TTTTGGGGTAAAAATGGGA-TTTTTGGAAG

                                          
        581 TTTTGGGGTCAAAAATGGGATTTTTGGAAG
          1 TTTTGGGGT-AAAAATGGGATTTTTGGAAG

              **             *    *  *   
        611 TTCGGGGGT-AAAATGGAATTTCTGAAAG
          1 TTTTGGGGTAAAAATGGGATTTTTGGAAG

                             *             
        639 TTTTGGGGTCAAAAATGAGACTTTTT-GAAG
          1 TTTTGGGGT-AAAAATGGGA-TTTTTGGAAG

              
        669 TT
          1 TT

        671 AGGGACCTCC


Statistics
Matches: 177,  Mismatches: 26, Indels: 12
        0.82            0.12        0.06

Matches are distributed among these distances:
  28   23  0.13
  29   35  0.20
  30  106  0.60
  31   13  0.07

ACGTcount: A:0.30, C:0.03, G:0.31, T:0.36


Consensus pattern (29 bp):   
TTTTGGGGTAAAAATGGGATTTTTGGAAG

Found at i:1912 original size:23 final size:21

Alignment explanation


    Indices: 1859--1908  Score: 84
    Period size: 20  Copynumber: 2.4  Consensus size: 21

       1849 TTTCCCTTTT

                        *        
       1859 TTATTATTAAAACATTATTTA
          1 TTATTATTAAAAAATTATTTA

                                 
       1880 TTATTATTAAAAAA-TATTTA
          1 TTATTATTAAAAAATTATTTA

                     
       1900 TTATTATTA
          1 TTATTATTA

       1909 TTAATATATT


Statistics
Matches: 28,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  20   15  0.54
  21   13  0.46

ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54


Consensus pattern (21 bp):   
TTATTATTAAAAAATTATTTA

Found at i:1927 original size:21 final size:21

Alignment explanation


    Indices: 1859--1929  Score: 79
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       1849 TTTCCCTTTT

                        *    *   
       1859 TTATTATTAAAACATTATTTA
          1 TTATTATTAAAATATTAATTA

                              *    
       1880 TTATTATTAAAAAATATTTATTA
          1 TTATTATT--AAAATATTAATTA

                      *         *
       1903 TTATTATTAATATATTAATTG
          1 TTATTATTAAAATATTAATTA

                  
       1924 TTATTA
          1 TTATTA

       1930 AATAATCATT


Statistics
Matches: 42,  Mismatches: 6, Indels: 4
        0.81            0.12        0.08

Matches are distributed among these distances:
  21   24  0.57
  23   18  0.43

ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55


Consensus pattern (21 bp):   
TTATTATTAAAATATTAATTA

Found at i:2655 original size:17 final size:17

Alignment explanation


    Indices: 2634--2691  Score: 80
    Period size: 17  Copynumber: 3.4  Consensus size: 17

       2624 TTTGGGCTTT

                       *     
       2634 ATTTAAATTTATAATAA
          1 ATTTAAATTTAAAATAA

            *                 
       2651 TTTTAAATTTGAAAATAA
          1 ATTTAAATTT-AAAATAA

                   *         
       2669 ATTTAAACTTAAAATAA
          1 ATTTAAATTTAAAATAA

                  
       2686 ATTTAA
          1 ATTTAA


Statistics
Matches: 36,  Mismatches: 4, Indels: 2
        0.86            0.10        0.05

Matches are distributed among these distances:
  17   22  0.61
  18   14  0.39

ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43


Consensus pattern (17 bp):   
ATTTAAATTTAAAATAA
Done.