Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010768.1 Kokia drynarioides strain JFW-HI SEQ_125729, 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: 33250
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35

Warning! 35 characters in sequence are not A, C, G, or T


Found at i:16274 original size:2 final size:2

Alignment explanation


    Indices: 16262--16293  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      16252 ACAGAACATG

                                                             
      16262 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      16294 GCATTGAGGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:19999 original size:4 final size:4

Alignment explanation


    Indices: 19990--20017  Score: 56
    Period size: 4  Copynumber: 7.0  Consensus size: 4

      19980 TGAAGGTTCT

                                              
      19990 GGTG GGTG GGTG GGTG GGTG GGTG GGTG
          1 GGTG GGTG GGTG GGTG GGTG GGTG GGTG

      20018 AGTCAGATGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   24  1.00

ACGTcount: A:0.00, C:0.00, G:0.75, T:0.25


Consensus pattern (4 bp):   
GGTG

Found at i:20191 original size:10 final size:8

Alignment explanation


    Indices: 20178--20204  Score: 54
    Period size: 8  Copynumber: 3.4  Consensus size: 8

      20168 ACACATCGGA

                    
      20178 CTCTCTGC
          1 CTCTCTGC

                    
      20186 CTCTCTGC
          1 CTCTCTGC

                    
      20194 CTCTCTGC
          1 CTCTCTGC

               
      20202 CTC
          1 CTC

      20205 AGACTCTTTC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   19  1.00

ACGTcount: A:0.00, C:0.52, G:0.11, T:0.37


Consensus pattern (8 bp):   
CTCTCTGC

Found at i:31501 original size:20 final size:19

Alignment explanation


    Indices: 31454--31501  Score: 51
    Period size: 20  Copynumber: 2.5  Consensus size: 19

      31444 TTTAAAAAAA

                    *      *   
      31454 TAAAATTTTAATAATGTTT
          1 TAAAATTTAAATAATATTT

              * *               
      31473 TACATTTTAAATATATATTT
          1 TAAAATTTAAATA-ATATTT

                     
      31493 TAAAATTTA
          1 TAAAATTTA

      31502 CCCTTTATTA


Statistics
Matches: 22,  Mismatches: 6, Indels: 1
        0.76            0.21        0.03

Matches are distributed among these distances:
  19   10  0.45
  20   12  0.55

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52


Consensus pattern (19 bp):   
TAAAATTTAAATAATATTT

Found at i:32925 original size:18 final size:18

Alignment explanation


    Indices: 32888--32924  Score: 58
    Period size: 17  Copynumber: 2.1  Consensus size: 18

      32878 TTGTTTTATA

                              
      32888 TTAATTTAATTTCATATT
          1 TTAATTTAATTTCATATT

                        *     
      32906 TTAA-TTAATTTGATATT
          1 TTAATTTAATTTCATATT

              
      32923 TT
          1 TT

      32925 TTGTATTTAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17   14  0.78
  18    4  0.22

ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62


Consensus pattern (18 bp):   
TTAATTTAATTTCATATT
Done.