Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006425.1 Kokia drynarioides strain JFW-HI SEQ_121007, 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: 21766
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:4632 original size:35 final size:35

Alignment explanation


    Indices: 4586--4666  Score: 162
    Period size: 35  Copynumber: 2.3  Consensus size: 35

       4576 TAGATTGAAG

                                               
       4586 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
          1 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA

                                               
       4621 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA
          1 TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA

                       
       4656 TGGTTGGTGAG
          1 TGGTTGGTGAG

       4667 ATGGTGGTGG


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   46  1.00

ACGTcount: A:0.36, C:0.00, G:0.42, T:0.22


Consensus pattern (35 bp):   
TGGTTGGTGAGGTGAGAAAATGGAAGAAAATGGAA

Found at i:8941 original size:23 final size:23

Alignment explanation


    Indices: 8904--8964  Score: 113
    Period size: 23  Copynumber: 2.6  Consensus size: 23

       8894 ATTTAATCTT

                                    
       8904 TTAAAAATTATAAATATATAACTA
          1 TTAAAAATTA-AAATATATAACTA

                                   
       8928 TTAAAAATTAAAATATATAACTA
          1 TTAAAAATTAAAATATATAACTA

                          
       8951 TTAAAAATTAAAAT
          1 TTAAAAATTAAAAT

       8965 TTAATTTCGA


Statistics
Matches: 37,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  23   27  0.73
  24   10  0.27

ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36


Consensus pattern (23 bp):   
TTAAAAATTAAAATATATAACTA

Found at i:9891 original size:25 final size:23

Alignment explanation


    Indices: 9863--9923  Score: 61
    Period size: 25  Copynumber: 2.6  Consensus size: 23

       9853 ATGATTCTAA

                         *           
       9863 AATATAAAAAAATTAAAAATTCAAT
          1 AATATAAAAAAATAAAAAATT--AT

                **                 
       9888 AATACGAAAAAATAAAAAATTAT
          1 AATATAAAAAAATAAAAAATTAT

                          
       9911 AAT-TAAAATAAAT
          1 AATATAAAA-AAAT

       9924 CATTAAAAAA


Statistics
Matches: 30,  Mismatches: 5, Indels: 4
        0.77            0.13        0.10

Matches are distributed among these distances:
  22    3  0.10
  23    9  0.30
  25   18  0.60

ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26


Consensus pattern (23 bp):   
AATATAAAAAAATAAAAAATTAT

Found at i:10982 original size:13 final size:15

Alignment explanation


    Indices: 10963--10998  Score: 51
    Period size: 13  Copynumber: 2.6  Consensus size: 15

      10953 TTTTTATATT

                           
      10963 TTAAAAAATGGAA-A
          1 TTAAAAAATGGAATA

                           
      10977 -TAAAAAA-GGAATA
          1 TTAAAAAATGGAATA

                     
      10990 TTAAAAAAT
          1 TTAAAAAAT

      10999 AAAAAAGGAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 5
        0.79            0.00        0.21

Matches are distributed among these distances:
  12    4  0.21
  13    8  0.42
  14    7  0.37

ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22


Consensus pattern (15 bp):   
TTAAAAAATGGAATA

Found at i:17147 original size:35 final size:35

Alignment explanation


    Indices: 17101--17181  Score: 162
    Period size: 35  Copynumber: 2.3  Consensus size: 35

      17091 CCACCACCAT

                                               
      17101 CTCACCAACCATTCCATTTTCTTCCATTTTCTCAC
          1 CTCACCAACCATTCCATTTTCTTCCATTTTCTCAC

                                               
      17136 CTCACCAACCATTCCATTTTCTTCCATTTTCTCAC
          1 CTCACCAACCATTCCATTTTCTTCCATTTTCTCAC

                       
      17171 CTCACCAACCA
          1 CTCACCAACCA

      17182 CTTCAATCTA


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   46  1.00

ACGTcount: A:0.22, C:0.42, G:0.00, T:0.36


Consensus pattern (35 bp):   
CTCACCAACCATTCCATTTTCTTCCATTTTCTCAC
Done.