Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003180.1 Kokia drynarioides strain JFW-HI SEQ_115787, 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: 45113
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34

Warning! 7 characters in sequence are not A, C, G, or T


Found at i:11 original size:2 final size:2

Alignment explanation


    Indices: 6--31  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

          1 AAAAA

                                                  
          6 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

         32 TCATTTCGTA


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

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:9604 original size:19 final size:20

Alignment explanation


    Indices: 9580--9617  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       9570 CATGTTGAGT

                         *      
       9580 AGTGAT-TGCATGGAAATCA
          1 AGTGATATGCATGCAAATCA

                               
       9599 AGTGATATGCATGCAAATC
          1 AGTGATATGCATGCAAATC

       9618 CCAGTTTTCT


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

Matches are distributed among these distances:
  19    6  0.35
  20   11  0.65

ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26


Consensus pattern (20 bp):   
AGTGATATGCATGCAAATCA

Found at i:26195 original size:30 final size:31

Alignment explanation


    Indices: 26161--26226  Score: 89
    Period size: 30  Copynumber: 2.2  Consensus size: 31

      26151 TAAAATAGGG

                                    *      
      26161 TTTTAAGTTCCTTAAAAGCT-GGATAATTTT
          1 TTTTAAGTTCCTTAAAAGCTAGGAAAATTTT

                 *            *   *        
      26191 TTTTAGGTTCCTTAAAAGTTAGTAAAATTTT
          1 TTTTAAGTTCCTTAAAAGCTAGGAAAATTTT

                 
      26222 TTTTA
          1 TTTTA

      26227 CCCCTTAAAA


Statistics
Matches: 31,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  30   18  0.58
  31   13  0.42

ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50


Consensus pattern (31 bp):   
TTTTAAGTTCCTTAAAAGCTAGGAAAATTTT

Found at i:39061 original size:2 final size:2

Alignment explanation


    Indices: 39056--39088  Score: 52
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      39046 TAATGCTAAT

                                                                
      39056 TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      39089 CGTAAAGTTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    2  0.07
   2   27  0.93

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


Consensus pattern (2 bp):   
TA

Found at i:42805 original size:57 final size:57

Alignment explanation


    Indices: 42736--42852  Score: 234
    Period size: 57  Copynumber: 2.1  Consensus size: 57

      42726 GTCTTGATGA

                                                                     
      42736 TAAGAAGTAAGCAAATTAAACTTCTTGTAGTAGACTTTGAATCCAATCAAAAGTTAT
          1 TAAGAAGTAAGCAAATTAAACTTCTTGTAGTAGACTTTGAATCCAATCAAAAGTTAT

                                                                     
      42793 TAAGAAGTAAGCAAATTAAACTTCTTGTAGTAGACTTTGAATCCAATCAAAAGTTAT
          1 TAAGAAGTAAGCAAATTAAACTTCTTGTAGTAGACTTTGAATCCAATCAAAAGTTAT

               
      42850 TAA
          1 TAA

      42853 TAGCAAACTT


Statistics
Matches: 60,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  57   60  1.00

ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32


Consensus pattern (57 bp):   
TAAGAAGTAAGCAAATTAAACTTCTTGTAGTAGACTTTGAATCCAATCAAAAGTTAT

Found at i:45065 original size:14 final size:14

Alignment explanation


    Indices: 45046--45076  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      45036 TGAATTTAAT

                          
      45046 AAAATTTAATTTTA
          1 AAAATTTAATTTTA

                          
      45060 AAAATTTAATTTTA
          1 AAAATTTAATTTTA

               
      45074 AAA
          1 AAA

      45077 TCTAAAAAGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (14 bp):   
AAAATTTAATTTTA

Done.