Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001645.1 Kokia drynarioides strain JFW-HI SEQ_113290, 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: 57142
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32

Warning! 64 characters in sequence are not A, C, G, or T


Found at i:35430 original size:6 final size:6

Alignment explanation


    Indices: 35419--35451  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

      35409 TTGCTTATAT

                                                  
      35419 CACCCC CACCCC CACCCC CACCCC CACCCC CAC
          1 CACCCC CACCCC CACCCC CACCCC CACCCC CAC

      35452 ATATATTAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00


Consensus pattern (6 bp):   
CACCCC

Found at i:40656 original size:2 final size:2

Alignment explanation


    Indices: 40649--40673  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      40639 GACTAGAATT

                                                 
      40649 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

      40674 GCAATGCGTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:54108 original size:29 final size:30

Alignment explanation


    Indices: 54053--54117  Score: 87
    Period size: 29  Copynumber: 2.2  Consensus size: 30

      54043 TTGTTTACAT

                                           
      54053 AAATAATATAAAAAATAAAAATTAATTACGA
          1 AAATAATATAAAAAAT-AAAATTAATTACGA

                *    *                 *  
      54084 AAATGATATGAAAAAT-AAATTAATTATGA
          1 AAATAATATAAAAAATAAAATTAATTACGA

                 
      54113 AAATA
          1 AAATA

      54118 GGTGTTTTTT


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  29   16  0.53
  31   14  0.47

ACGTcount: A:0.65, C:0.02, G:0.06, T:0.28


Consensus pattern (30 bp):   
AAATAATATAAAAAATAAAATTAATTACGA

Found at i:54861 original size:28 final size:27

Alignment explanation


    Indices: 54829--54889  Score: 77
    Period size: 28  Copynumber: 2.2  Consensus size: 27

      54819 TAACAAATAC

                   *                    
      54829 TTATTTCGTAATTAATCTATTTTTCATA
          1 TTATTTCATAATTAAT-TATTTTTCATA

                   *                *   
      54857 TTATTTTTATAATTAATTATTTTTTATA
          1 TTA-TTTCATAATTAATTATTTTTCATA

                 
      54885 TTATT
          1 TTATT

      54890 GGATAAAAAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 3
        0.83            0.09        0.09

Matches are distributed among these distances:
  27    2  0.07
  28   16  0.55
  29   11  0.38

ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64


Consensus pattern (27 bp):   
TTATTTCATAATTAATTATTTTTCATA
Done.