Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014615.1 Kokia drynarioides strain JFW-HI SEQ_129654, 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: 24558
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--37  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

                                                                   
          1 TA TA 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 TA TA T

         38 GTTATTATAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:1026 original size:29 final size:31

Alignment explanation


    Indices: 979--1036  Score: 75
    Period size: 29  Copynumber: 1.9  Consensus size: 31

        969 AAATGATAAT

                          *    *  *        
        979 TTTTAATTTAAACTTTTTATAATTTATAAGA
          1 TTTTAATTTAAACTCTTTAAAAATTATAAGA

                                         
       1010 TTTT-ATTT-AACTCTTTAAAAATTATAA
          1 TTTTAATTTAAACTCTTTAAAAATTATAA

       1037 ATACATAAAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  29   16  0.67
  30    4  0.17
  31    4  0.17

ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53


Consensus pattern (31 bp):   
TTTTAATTTAAACTCTTTAAAAATTATAAGA

Found at i:8639 original size:18 final size:19

Alignment explanation


    Indices: 8618--8663  Score: 60
    Period size: 20  Copynumber: 2.5  Consensus size: 19

       8608 TTATAAAATA

                               
       8618 ATATTATAT-TAATTATAT
          1 ATATTATATATAATTATAT

                  *             
       8636 ATATTAAATGATAATTATAT
          1 ATATTATAT-ATAATTATAT

                     
       8656 AT-TTATAT
          1 ATATTATAT

       8664 CTATATTAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  18    8  0.33
  19    5  0.21
  20   11  0.46

ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52


Consensus pattern (19 bp):   
ATATTATATATAATTATAT

Found at i:8933 original size:16 final size:16

Alignment explanation


    Indices: 8914--8944  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       8904 ATTTTTTTAA

                     *      
       8914 AAAAATAATTTTAAAT
          1 AAAAATAATCTTAAAT

                           
       8930 AAAAATAATCTTAAA
          1 AAAAATAATCTTAAA

       8945 AAATTAAATA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32


Consensus pattern (16 bp):   
AAAAATAATCTTAAAT

Found at i:9323 original size:21 final size:22

Alignment explanation


    Indices: 9277--9320  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       9267 TTATAATTAT

                                  
       9277 ATATTTTAGAATTTTATAAAAA
          1 ATATTTTAGAATTTTATAAAAA

                            *      
       9299 ATATTTTA-AATTTCTTTAAAAA
          1 ATATTTTAGAATTT-TATAAAAA

       9321 TATGTATTAT


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

Matches are distributed among these distances:
  21    5  0.25
  22   15  0.75

ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48


Consensus pattern (22 bp):   
ATATTTTAGAATTTTATAAAAA

Found at i:13797 original size:23 final size:22

Alignment explanation


    Indices: 13767--13888  Score: 115
    Period size: 23  Copynumber: 5.4  Consensus size: 22

      13757 GCTGGGGAAA

                                   
      13767 CAGTAAGCACACACAGTGC-AAT
          1 CAGTAAGCACACA-AGTGCGAAT

                                    
      13789 CCAGTAAGCACACACAGTGC-AAT
          1 -CAGTAAGCACACA-AGTGCGAAT

            *    *                  
      13812 TAGTAGGCACACAAGGTGCGAAAT
          1 CAGTAAGCACACAA-GTGCG-AAT

                                  *
      13836 -AGTAAGCACACGAAGTGCGAAA
          1 CAGTAAGCACAC-AAGTGCGAAT

                                  *
      13858 CAGTAAGCACACGAAGTGCGAAA
          1 CAGTAAGCACAC-AAGTGCGAAT

              *     
      13881 CAATAAGC
          1 CAGTAAGC

      13889 GCGCTTGCGT


Statistics
Matches: 89,  Mismatches: 5, Indels: 10
        0.86            0.05        0.10

Matches are distributed among these distances:
  21    1  0.01
  22   17  0.19
  23   66  0.74
  24    5  0.06

ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12


Consensus pattern (22 bp):   
CAGTAAGCACACAAGTGCGAAT
Done.