Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011377.1 Kokia drynarioides strain JFW-HI SEQ_126358, 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: 55528
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33

Warning! 38 characters in sequence are not A, C, G, or T


Found at i:9182 original size:21 final size:21

Alignment explanation


    Indices: 9156--9203  Score: 96
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       9146 GATGTTTGGG

                                 
       9156 AAATGCATAAACAACAACAGC
          1 AAATGCATAAACAACAACAGC

                                 
       9177 AAATGCATAAACAACAACAGC
          1 AAATGCATAAACAACAACAGC

                  
       9198 AAATGC
          1 AAATGC

       9204 TTGTTCAATT


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

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.56, C:0.23, G:0.10, T:0.10


Consensus pattern (21 bp):   
AAATGCATAAACAACAACAGC

Found at i:12074 original size:2 final size:2

Alignment explanation


    Indices: 12067--12099  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      12057 TAGGATAAAC

                                                             
      12067 TA TA TA TA 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 TA TA TA TA T

      12100 TTATTTTTTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:43509 original size:26 final size:28

Alignment explanation


    Indices: 43480--43534  Score: 78
    Period size: 28  Copynumber: 2.0  Consensus size: 28

      43470 TGTACTTTTG

                                *       
      43480 TATATTT-AG-AATTTAGTCTCTATACT
          1 TATATTTCAGAAATTTAGTCCCTATACT

                                   *    
      43506 TATATTTCAGAAATTTAGTCCCTTTACT
          1 TATATTTCAGAAATTTAGTCCCTATACT

             
      43534 T
          1 T

      43535 TTTTATATTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  26    7  0.28
  27    2  0.08
  28   16  0.64

ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49


Consensus pattern (28 bp):   
TATATTTCAGAAATTTAGTCCCTATACT

Found at i:53927 original size:21 final size:20

Alignment explanation


    Indices: 53897--53940  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 20

      53887 TTTTATCGGT

                       *    *   
      53897 AAAAGTAAAATTAATTTTTA
          1 AAAAGTAAAATGAATTATTA

                                 
      53917 AAAAGATAAAATGAATTATTA
          1 AAAAG-TAAAATGAATTATTA

               
      53938 AAA
          1 AAA

      53941 TAAAAAATTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20    5  0.24
  21   16  0.76

ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32


Consensus pattern (20 bp):   
AAAAGTAAAATGAATTATTA

Found at i:53940 original size:20 final size:19

Alignment explanation


    Indices: 53896--53957  Score: 58
    Period size: 21  Copynumber: 3.3  Consensus size: 19

      53886 CTTTTATCGG

                        *    * 
      53896 TAAAAGTAAAATTAATTTT
          1 TAAAAGTAAAATGAATTAT

                                 
      53915 TAAAAAGATAAAATGAATTAT
          1 T-AAAAG-TAAAATGAATTAT

                                
      53936 TAAAA-TAAAA--AATTTAT
          1 TAAAAGTAAAATGAA-TTAT

                 
      53953 TAAAA
          1 TAAAA

      53958 TTTAGTAACT


Statistics
Matches: 38,  Mismatches: 2, Indels: 8
        0.79            0.04        0.17

Matches are distributed among these distances:
  16    2  0.05
  17    9  0.24
  18    5  0.13
  19    1  0.03
  20    9  0.24
  21   12  0.32

ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34


Consensus pattern (19 bp):   
TAAAAGTAAAATGAATTAT
Done.