Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002731.1 Kokia drynarioides strain JFW-HI SEQ_115035, 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: 18693
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35


Found at i:3518 original size:23 final size:23

Alignment explanation


    Indices: 3465--3519  Score: 101
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       3455 ACCGGAGAAC

                   *               
       3465 ACGTGTTAAGTCTATGAGAATAT
          1 ACGTGTTGAGTCTATGAGAATAT

                                   
       3488 ACGTGTTGAGTCTATGAGAATAT
          1 ACGTGTTGAGTCTATGAGAATAT

                     
       3511 ACGTGTTGA
          1 ACGTGTTGA

       3520 CATGTATGGA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  23   31  1.00

ACGTcount: A:0.31, C:0.09, G:0.25, T:0.35


Consensus pattern (23 bp):   
ACGTGTTGAGTCTATGAGAATAT

Found at i:15092 original size:23 final size:25

Alignment explanation


    Indices: 15049--15094  Score: 69
    Period size: 23  Copynumber: 1.9  Consensus size: 25

      15039 ATTGGATCCA

                            *        
      15049 AATTAAATTCTAAAATGATAATTAG
          1 AATTAAATTCTAAAATAATAATTAG

                                   
      15074 AATTAAA-TCT-AAATAATAATT
          1 AATTAAATTCTAAAATAATAATT

      15095 CCCTAATTGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  23   10  0.50
  24    3  0.15
  25    7  0.35

ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37


Consensus pattern (25 bp):   
AATTAAATTCTAAAATAATAATTAG

Found at i:15295 original size:19 final size:19

Alignment explanation


    Indices: 15271--15317  Score: 76
    Period size: 19  Copynumber: 2.5  Consensus size: 19

      15261 TTTATATATA

                               
      15271 TGCTTTTTGACACAAATTT
          1 TGCTTTTTGACACAAATTT

                       *       
      15290 TGCTTTTTGACCCAAATTT
          1 TGCTTTTTGACACAAATTT

             *       
      15309 TCCTTTTTG
          1 TGCTTTTTG

      15318 TCTTCGATTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  19   26  1.00

ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51


Consensus pattern (19 bp):   
TGCTTTTTGACACAAATTT

Found at i:16787 original size:27 final size:29

Alignment explanation


    Indices: 16738--16797  Score: 72
    Period size: 27  Copynumber: 2.1  Consensus size: 29

      16728 ATTTTTTAAA

                                   *  *  
      16738 AAATATAATTTATTTTTATTTAATATTTT
          1 AAATATAATTTATTTTTATTTAAAATCTT

                                          
      16767 AAATA-AATTT-TCTTTTA-TTAAAATCTT
          1 AAATATAATTTAT-TTTTATTTAAAATCTT

                
      16794 AAAT
          1 AAAT

      16798 TCAGACAACT


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  27   13  0.46
  28   10  0.36
  29    5  0.18

ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55


Consensus pattern (29 bp):   
AAATATAATTTATTTTTATTTAAAATCTT

Found at i:18058 original size:161 final size:161

Alignment explanation


    Indices: 17793--18116  Score: 639
    Period size: 161  Copynumber: 2.0  Consensus size: 161

      17783 GGTTTGATGT

                                                                             
      17793 TACAATCGCGTTGAGTTGATCTACTGATTCCTCAAAGCAAAAAAAACACCTACTTTCACTACCGT
          1 TACAATCGCGTTGAGTTGATCTACTGATTCCTCAAAGCAAAAAAAACACCTACTTTCACTACCGT

                                                                             
      17858 TTATGGGATGCAGTTTGGCAGGTCTGGAATACAATTAGCAATGGCACGTATTTCCCACTTATTTT
         66 TTATGGGATGCAGTTTGGCAGGTCTGGAATACAATTAGCAATGGCACGTATTTCCCACTTATTTT

                                           
      17923 TCTGCTTTCGCTGTTGAAGTTGATATACCCA
        131 TCTGCTTTCGCTGTTGAAGTTGATATACCCA

                                                            *                
      17954 TACAATCGCGTTGAGTTGATCTACTGATTCCTCAAAGCAAAAAAAACATCTACTTTCACTACCGT
          1 TACAATCGCGTTGAGTTGATCTACTGATTCCTCAAAGCAAAAAAAACACCTACTTTCACTACCGT

                                                                             
      18019 TTATGGGATGCAGTTTGGCAGGTCTGGAATACAATTAGCAATGGCACGTATTTCCCACTTATTTT
         66 TTATGGGATGCAGTTTGGCAGGTCTGGAATACAATTAGCAATGGCACGTATTTCCCACTTATTTT

                                           
      18084 TCTGCTTTCGCTGTTGAAGTTGATATACCCA
        131 TCTGCTTTCGCTGTTGAAGTTGATATACCCA

              
      18115 TA
          1 TA

      18117 GGATAGGAGC


Statistics
Matches: 162,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 161  162  1.00

ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33


Consensus pattern (161 bp):   
TACAATCGCGTTGAGTTGATCTACTGATTCCTCAAAGCAAAAAAAACACCTACTTTCACTACCGT
TTATGGGATGCAGTTTGGCAGGTCTGGAATACAATTAGCAATGGCACGTATTTCCCACTTATTTT
TCTGCTTTCGCTGTTGAAGTTGATATACCCA

Found at i:18641 original size:6 final size:6

Alignment explanation


    Indices: 18632--18677  Score: 74
    Period size: 6  Copynumber: 7.7  Consensus size: 6

      18622 TGGGGACAAG

                                                    *      *     
      18632 GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTG GTGGTG GTGG
          1 GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGGTA GTGG

      18678 AGGAGGAGGA


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
   6   39  1.00

ACGTcount: A:0.11, C:0.00, G:0.57, T:0.33


Consensus pattern (6 bp):   
GTGGTA

Done.