Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006568.1 Kokia drynarioides strain JFW-HI SEQ_121154, 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, 984

Length: 1641
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37


Found at i:825 original size:15 final size:17

Alignment explanation


    Indices: 798--874  Score: 72
    Period size: 16  Copynumber: 4.6  Consensus size: 17

        788 AAAATAAAAT

                  *          
        798 TTAATTAAAAGAAGAAA
          1 TTAATTTAAAGAAGAAA

                         *   
        815 -T-ATTTAAAGAATAAA
          1 TTAATTTAAAGAAGAAA

                          *   
        830 TTAATTTAAAGTAATAAA
          1 TTAATTTAAAG-AAGAAA

                              
        848 TTAAATTTAAA-AA-AAA
          1 TT-AATTTAAAGAAGAAA

                       
        864 TATAATTTAAA
          1 T-TAATTTAAA

        875 TTAACTAAGA


Statistics
Matches: 53,  Mismatches: 2, Indels: 11
        0.80            0.03        0.17

Matches are distributed among these distances:
  15   12  0.23
  16   14  0.26
  17   11  0.21
  18    8  0.15
  19    8  0.15

ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34


Consensus pattern (17 bp):   
TTAATTTAAAGAAGAAA

Found at i:871 original size:72 final size:73

Alignment explanation


    Indices: 788--953  Score: 185
    Period size: 75  Copynumber: 2.2  Consensus size: 73

        778 TTTAAATTGC

                  *                                                          
        788 AAAATAAAATTTAATTAAAAGAAGAAATATTTAAAG-AATAAATTAATTTAAAGTAATAAA-TTA
          1 AAAATATAATTTAATTAAAAGAAGAAATATTTAAAGAAATAAATTAATTTAAAGTAATAAACTT-

                     
        851 AATTTAAAA
         65 AATTTAAAA

                                **    *                      *               
        860 AAAATATAATTTAAATT-AACTAAGACATATTTAAAGAATAATAAATTATTTTAAAGTAATAAAC
          1 AAAATATAATTT-AATTAAAAGAAGAAATATTTAAAG-A-AATAAATTAATTTAAAGTAATAAAC

               *       
        924 TTAGTTTAAAA
         63 TTAATTTAAAA

               *         *     
        935 ATATATATTAATTGAATTA
          1 A-AAATA-TAATTTAATTA

        954 TGAAATTGTT


Statistics
Matches: 78,  Mismatches: 8, Indels: 11
        0.80            0.08        0.11

Matches are distributed among these distances:
  72   27  0.35
  73    4  0.05
  75   32  0.41
  76   10  0.13
  77    5  0.06

ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36


Consensus pattern (73 bp):   
AAAATATAATTTAATTAAAAGAAGAAATATTTAAAGAAATAAATTAATTTAAAGTAATAAACTTA
ATTTAAAA

Found at i:892 original size:36 final size:36

Alignment explanation


    Indices: 809--921  Score: 108
    Period size: 36  Copynumber: 3.1  Consensus size: 36

        799 TAATTAAAAG

                                                
        809 AAGAAATATTTAAAGAATAAATTAATTTAAAGTAAT
          1 AAGAAATATTTAAAGAATAAATTAATTTAAAGTAAT

                                              *     
        845 AA-ATTAA-ATTTAAA-AA-AAATATAATTTAAATTAACT
          1 AAGA--AATATTTAAAGAATAAAT-TAATTTAAAGTAA-T

                *                      *           
        881 AAGACATATTTAAAGAATAATAAATTATTTTAAAGTAAT
          1 AAGAAATATTTAAAG---AATAAATTAATTTAAAGTAAT

              
        920 AA
          1 AA

        922 ACTTAGTTTA


Statistics
Matches: 62,  Mismatches: 4, Indels: 19
        0.73            0.05        0.22

Matches are distributed among these distances:
  34    4  0.06
  35   16  0.26
  36   19  0.31
  37    3  0.05
  39    3  0.05
  40   13  0.21
  41    4  0.06

ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35


Consensus pattern (36 bp):   
AAGAAATATTTAAAGAATAAATTAATTTAAAGTAAT

Found at i:912 original size:20 final size:21

Alignment explanation


    Indices: 889--937  Score: 61
    Period size: 19  Copynumber: 2.5  Consensus size: 21

        879 CTAAGACATA

                                *
        889 TTTAAAGAATAATAAA-TTAT
          1 TTTAAAGAATAATAAACTTAG

                                 
        909 TTTAAAG--TAATAAACTTAG
          1 TTTAAAGAATAATAAACTTAG

                       
        928 TTTAAA-AATA
          1 TTTAAAGAATA

        938 TATATTAATT


Statistics
Matches: 25,  Mismatches: 1, Indels: 6
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    7  0.28
  19    9  0.36
  20    9  0.36

ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39


Consensus pattern (21 bp):   
TTTAAAGAATAATAAACTTAG
Done.