Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010887.1 Kokia drynarioides strain JFW-HI SEQ_125855, 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: 4642
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.33

Warning! 58 characters in sequence are not A, C, G, or T


Found at i:430 original size:95 final size:94

Alignment explanation


    Indices: 331--628  Score: 309
    Period size: 95  Copynumber: 3.1  Consensus size: 94

        321 NNNNNNNNNN

                         *                                       * *         
        331 AGTGGAGCAAGATGAAGCCACACCAAATCCTATCTTCCTGAAGTTGCAGTGAAGCAGATTAAAGT
          1 AGTGGAGCAAGATAAAG-CACACCAAATCCTATCTTCCTGAAGTTGCAGTGAAACGGATTAAAGT

                 *                *       
        396 AGTAGTAAATCTTTATCTCCTTAAAGTTGC
         65 AGTAGCAAATCTTTATCTCCTTGAAGTTGC

                   *           *  *          *     *              *          
        426 AGTGGAGAAAGATAAAGC-TA-TAAATCCTAT-ATCCTTAAAGTTGCAAG-G-ATCGGATTAAAA
          1 AGTGGAGCAAGATAAAGCACACCAAATCCTATCTTCC-TGAAGTTGC-AGTGAAACGGATT-AAA

            *     * *   *            *         
        486 CTAACATTGGCAGATCTTTATCTCCCTGAAGTTGC
         63 GT---AGTAGCAAATCTTTATCTCCTTGAAGTTGC

                                                     *                      *
        521 AGTGGAGCAAGATAAAGTCACACCAAATCCTATCTTCCTGAGGTTGCAGTGAAACGGATTAAAGC
          1 AGTGGAGCAAGATAAAG-CACACCAAATCCTATCTTCCTGAAGTTGCAGTGAAACGGATTAAAGT

                  *                      *
        586 AGTAGCGAATCTTTATCTCCTTGAAGTTGT
         65 AGTAGCAAATCTTTATCTCCTTGAAGTTGC

                         
        616 AGTGGAGCAAGAT
          1 AGTGGAGCAAGAT

        629 GAAGTTACAA


Statistics
Matches: 161,  Mismatches: 30, Indels: 24
        0.75            0.14        0.11

Matches are distributed among these distances:
  91    9  0.06
  92   22  0.14
  93    3  0.02
  94    1  0.01
  95   92  0.57
  96    1  0.01
  97    3  0.02
  98   20  0.12
  99   10  0.06

ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27


Consensus pattern (94 bp):   
AGTGGAGCAAGATAAAGCACACCAAATCCTATCTTCCTGAAGTTGCAGTGAAACGGATTAAAGTA
GTAGCAAATCTTTATCTCCTTGAAGTTGC

Found at i:442 original size:48 final size:44

Alignment explanation


    Indices: 371--470  Score: 103
    Period size: 48  Copynumber: 2.2  Consensus size: 44

        361 TATCTTCCTG

                          *           *          *   *      
        371 AAGTTGCAGTGAAGCAGATTAAAGTAGTAGTAAATCTTTATCTCCTTA
          1 AAGTTGCAGTGAAGAAGATTAAAG--CTA-TAAATC-CTATATCCTTA

                       *                                 
        419 AAGTTGCAGTGGAGAAAGA-TAAAGCTATAAATCCTATATCCTTA
          1 AAGTTGCAGTGAAG-AAGATTAAAGCTATAAATCCTATATCCTTA

                    
        463 AAGTTGCA
          1 AAGTTGCA

        471 AGGATCGGAT


Statistics
Matches: 46,  Mismatches: 5, Indels: 6
        0.81            0.09        0.11

Matches are distributed among these distances:
  44   17  0.37
  45    6  0.13
  46    2  0.04
  48   18  0.39
  49    3  0.07

ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30


Consensus pattern (44 bp):   
AAGTTGCAGTGAAGAAGATTAAAGCTATAAATCCTATATCCTTA

Found at i:749 original size:50 final size:50

Alignment explanation


    Indices: 642--768  Score: 150
    Period size: 50  Copynumber: 2.5  Consensus size: 50

        632 GTTACAACAC

                        *      *          *                   
        642 CAAATCTTATATCCTTGAACTTGCAAGAATTGGATTAAAACTAAAATTGA
          1 CAAATCTTATATTCTTGAAGTTGCAAGAATCGGATTAAAACTAAAATTGA

              *                        *          *     *     
        692 CATATCTTATATTCTTGAAGTTGCAAGGATCGGATTAATACTAACATT-A
          1 CAAATCTTATATTCTTGAAGTTGCAAGAATCGGATTAAAACTAAAATTGA

                                         
        741 GCAAATCTT-TATCTACTTGAAGTTGCAA
          1 -CAAATCTTATAT-T-CTTGAAGTTGCAA

        769 TGGAGCAAGA


Statistics
Matches: 66,  Mismatches: 8, Indels: 5
        0.84            0.10        0.06

Matches are distributed among these distances:
  49    4  0.06
  50   49  0.74
  51   13  0.20

ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35


Consensus pattern (50 bp):   
CAAATCTTATATTCTTGAAGTTGCAAGAATCGGATTAAAACTAAAATTGA

Found at i:1639 original size:22 final size:23

Alignment explanation


    Indices: 1611--1657  Score: 94
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1601 TTTTTCAAGG

                                   
       1611 TAAAAAAAAAATTGCATCTTTAC
          1 TAAAAAAAAAATTGCATCTTTAC

                                   
       1634 TAAAAAAAAAATTGCATCTTTAC
          1 TAAAAAAAAAATTGCATCTTTAC

             
       1657 T
          1 T

       1658 TTAAGAAATT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32


Consensus pattern (23 bp):   
TAAAAAAAAAATTGCATCTTTAC
Done.