Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001042.1 Kokia drynarioides strain JFW-HI SEQ_112272, 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: 52613
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34

Warning! 168 characters in sequence are not A, C, G, or T


Found at i:28462 original size:12 final size:11

Alignment explanation


    Indices: 28426--28463  Score: 53
    Period size: 9  Copynumber: 3.5  Consensus size: 11

      28416 AAAACGCATA

                       
      28426 AAAATAACATC
          1 AAAATAACATC

                       
      28437 AAAATAAC--C
          1 AAAATAACATC

                        
      28446 AAAATAACAATC
          1 AAAATAAC-ATC

                  
      28458 AAAATA
          1 AAAATA

      28464 TCAGCAAAAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
   9    9  0.38
  11    8  0.33
  12    7  0.29

ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16


Consensus pattern (11 bp):   
AAAATAACATC

Found at i:40203 original size:19 final size:18

Alignment explanation


    Indices: 40175--40211  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

      40165 AAATGTTAAT

                               
      40175 AAAAACTATTTATTTAAAA
          1 AAAAACTATTT-TTTAAAA

                 *            
      40194 AAAAATTATTTTTTAAAA
          1 AAAAACTATTTTTTAAAA

      40212 CATTTGCTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    7  0.41
  19   10  0.59

ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41


Consensus pattern (18 bp):   
AAAAACTATTTTTTAAAA

Found at i:43114 original size:20 final size:18

Alignment explanation


    Indices: 43084--43127  Score: 52
    Period size: 18  Copynumber: 2.3  Consensus size: 18

      43074 TTATGTTCAC

                                 
      43084 ATTTGTAATTTAATCATTTTT
          1 ATTT-TAATTTAA-CA-TTTT

                      *       
      43105 ATTTTAATTTGACATTTT
          1 ATTTTAATTTAACATTTT

                 
      43123 ATTTT
          1 ATTTT

      43128 TATAATATTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  18    9  0.41
  19    2  0.09
  20    7  0.32
  21    4  0.18

ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64


Consensus pattern (18 bp):   
ATTTTAATTTAACATTTT

Found at i:52320 original size:68 final size:68

Alignment explanation


    Indices: 52240--52391  Score: 286
    Period size: 68  Copynumber: 2.2  Consensus size: 68

      52230 ATGTTTTATT

                   *                                           *             
      52240 TTAAGATTTAAAAAAATAAATTAATTTTCGAGAGTGTATGAAAATATATTTGATTGAGCGAATTT
          1 TTAAGATGTAAAAAAATAAATTAATTTTCGAGAGTGTATGAAAATATATTTAATTGAGCGAATTT

               
      52305 TTA
         66 TTA

                                                                             
      52308 TTAAGATGTAAAAAAATAAATTAATTTTCGAGAGTGTATGAAAATATATTTAATTGAGCGAATTT
          1 TTAAGATGTAAAAAAATAAATTAATTTTCGAGAGTGTATGAAAATATATTTAATTGAGCGAATTT

               
      52373 TTA
         66 TTA

                            
      52376 TTAAGATGTAAAAAAA
          1 TTAAGATGTAAAAAAA

      52392 GAACATTCAA


Statistics
Matches: 82,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  68   82  1.00

ACGTcount: A:0.45, C:0.03, G:0.14, T:0.38


Consensus pattern (68 bp):   
TTAAGATGTAAAAAAATAAATTAATTTTCGAGAGTGTATGAAAATATATTTAATTGAGCGAATTT
TTA
Done.