Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001137.1 Kokia drynarioides strain JFW-HI SEQ_112432, 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, 817

Length: 1362
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36


Found at i:94 original size:20 final size:21

Alignment explanation


    Indices: 69--110  Score: 68
    Period size: 20  Copynumber: 2.0  Consensus size: 21

         59 CATTAAAAAC

                                 
         69 TTTTTTAAATAAAT-TTTAAA
          1 TTTTTTAAATAAATGTTTAAA

                   *             
         89 TTTTTTATATAAATGTTTAAA
          1 TTTTTTAAATAAATGTTTAAA

             
        110 T
          1 T

        111 ATTATCCTTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  20   13  0.65
  21    7  0.35

ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57


Consensus pattern (21 bp):   
TTTTTTAAATAAATGTTTAAA

Found at i:664 original size:59 final size:58

Alignment explanation


    Indices: 542--739  Score: 243
    Period size: 59  Copynumber: 3.3  Consensus size: 58

        532 CTTGACTAAC

                *              *         *                               
        542 AATTAATTTCAATGGAGGTAGGTCCATGTGATGTTATATATATAAACAATTAGTTTATGCA
          1 AATTGATTTCAATGGAGGTGGGTCCATGTAATG---TATATATAAACAATTAGTTTATGCA

                     *                                  *         *    
        603 AATTGATTTTAATGGAGGTGGGTCCATGTAATGTGATATATAAATAATTAGTTTTTGCA
          1 AATTGATTTCAATGGAGGTGGGTCCATGTAATGT-ATATATAAACAATTAGTTTATGCA

                                              *                      *    
        662 AATTGATTTCAATGGAGGTGGGTCCATGTGATATATATTTATATAAACAATTAGTTTGTGCA
          1 AATTGATTTCAATGGAGGTGGGTCCATGT-A-ATGTA--TATATAAACAATTAGTTTATGCA

                     *      
        724 AATTGATTTAAATGGA
          1 AATTGATTTCAATGGA

        740 TAGGTCCTTT


Statistics
Matches: 121,  Mismatches: 11, Indels: 9
        0.86            0.08        0.06

Matches are distributed among these distances:
  58    1  0.01
  59   50  0.41
  60    2  0.02
  61   32  0.26
  62   36  0.30

ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39


Consensus pattern (58 bp):   
AATTGATTTCAATGGAGGTGGGTCCATGTAATGTATATATAAACAATTAGTTTATGCA

Found at i:844 original size:26 final size:26

Alignment explanation


    Indices: 799--873  Score: 80
    Period size: 26  Copynumber: 2.7  Consensus size: 26

        789 TTTAAGTTTA

                                           
        799 TTAAAAATTGAAGAAAAAAAATTTTAAATC-
          1 TTAAAAATT-AA-AAAAAAAA--TT-AATCT

                       *          *   
        829 TTAAAAATTAATAAAAAAATTATTCT
          1 TTAAAAATTAAAAAAAAAATTAATCT

                               
        855 TTAAAAATTAAAAAAAAAA
          1 TTAAAAATTAAAAAAAAAA

        874 ATAAAATTTT


Statistics
Matches: 41,  Mismatches: 3, Indels: 6
        0.82            0.06        0.12

Matches are distributed among these distances:
  25    3  0.07
  26   20  0.49
  28    7  0.17
  29    2  0.05
  30    9  0.22

ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31


Consensus pattern (26 bp):   
TTAAAAATTAAAAAAAAAATTAATCT
Done.