Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003466.1 Kokia drynarioides strain JFW-HI SEQ_116265, 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: 4247
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:4026 original size:87 final size:87

Alignment explanation


    Indices: 3928--4088  Score: 270
    Period size: 87  Copynumber: 1.9  Consensus size: 87

       3918 ATCCTAATTC

                                  *                        *                 
       3928 AAACTTTTGATAATAATTAATATAAATTATAAAATTTAATTTATAATTAATATTAA-AGATTATC
          1 AAACTTTTGATAATAATTAATAAAAATTATAAAATTTAATTTATAATCAATATTAAGA-ATTATC

              *                    
       3992 AACACTTTGAAAAAATTAAATGA
         65 AAAACTTTGAAAAAATTAAATGA

                                                               *             
       4015 AAACTTTTGATAATAATTAATAAAAATTATAAAATTTAATTTATAATCAATGTTAAGAATTATCA
          1 AAACTTTTGATAATAATTAATAAAAATTATAAAATTTAATTTATAATCAATATTAAGAATTATCA

                     
       4080 AAACTTTGA
         66 AAACTTTGA

       4089 GAAAGAAAAA


Statistics
Matches: 69,  Mismatches: 4, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  87   68  0.99
  88    1  0.01

ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39


Consensus pattern (87 bp):   
AAACTTTTGATAATAATTAATAAAAATTATAAAATTTAATTTATAATCAATATTAAGAATTATCA
AAACTTTGAAAAAATTAAATGA

Found at i:4040 original size:23 final size:23

Alignment explanation


    Indices: 3997--4040  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       3987 TTATCAACAC

                            *      
       3997 TTTGAAAAAATTAAATGAAAACT
          1 TTTGAAAAAATTAAATAAAAACT

                    *             
       4020 TTTGATAATAATT-AATAAAAA
          1 TTTGA-AAAAATTAAATAAAAA

       4041 TTATAAAATT


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  23   12  0.67
  24    6  0.33

ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34


Consensus pattern (23 bp):   
TTTGAAAAAATTAAATAAAAACT

Found at i:4204 original size:102 final size:101

Alignment explanation


    Indices: 4007--4191  Score: 257
    Period size: 102  Copynumber: 1.8  Consensus size: 101

       3997 TTTGAAAAAA

                 *     * *                                             *    *
       4007 TTAAATGAAAACTTTTGATAATAATTAATAAAAATTATAAAATTTAATTTATAATCAATGTTAAG
          1 TTAAAAGAAAAATCTTGATAATAATTAATAAAAATTATAAAATTTAATTTAT-ATCAATATTAAA

                             *                   
       4072 AATTATCAAAACTTTGAGAAAGAAAAAAAATAAGAAT
         65 AATTATCAAAACTTTGAAAAAGAAAAAAAATAAGAAT

                                   *      *                                  
       4109 TTAAAAGAAAAATCTTGATAATAGTTAATATAAATTATAAAATTTAATTTAT-T-AATATTAAAA
          1 TTAAAAGAAAAATCTTGATAATAATTAATAAAAATTATAAAATTTAATTTATATCAATATTAAAA

                    * *         
       4172 ATTATCAATATTTTGAAAAA
         66 ATTATCAAAACTTTGAAAAA

       4192 TGAAGAACAA


Statistics
Matches: 73,  Mismatches: 10, Indels: 3
        0.85            0.12        0.03

Matches are distributed among these distances:
  99   25  0.34
 100    1  0.01
 102   47  0.64

ACGTcount: A:0.54, C:0.03, G:0.06, T:0.36


Consensus pattern (101 bp):   
TTAAAAGAAAAATCTTGATAATAATTAATAAAAATTATAAAATTTAATTTATATCAATATTAAAA
ATTATCAAAACTTTGAAAAAGAAAAAAAATAAGAAT
Done.