Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002180.1 Kokia drynarioides strain JFW-HI SEQ_114146, 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: 4801
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:3762 original size:3 final size:3

Alignment explanation


    Indices: 3754--3790  Score: 74
    Period size: 3  Copynumber: 12.3  Consensus size: 3

       3744 ATTTACAAAT

                                                             
       3754 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A

       3791 AATTTTTCTT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   34  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
ATA

Found at i:3961 original size:19 final size:17

Alignment explanation


    Indices: 3938--4056  Score: 64
    Period size: 18  Copynumber: 6.5  Consensus size: 17

       3928 TTCTTTATTT

                              
       3938 TTTTATATTTTTTAATCA
          1 TTTTATATTTTTTAAT-A

                                 
       3956 TATTTATGAGTTTTTATAA-A
          1 T-TTTAT-A-TTTTT-TAATA

                      *        
       3976 -TTTATATCAATTTTAATA
          1 TTTTATAT--TTTTTAATA

                *             
       3994 TTTTGTATTTTTTAATAA
          1 TTTTATATTTTTTAAT-A

                               
       4012 TTTTATGA-TTTTTAATGA
          1 TTTTAT-ATTTTTTAAT-A

                     *       * 
       4030 TTTTTATAAGTTTTTAAGA
          1 -TTTTAT-ATTTTTTAATA

            *       
       4049 ATTTATAT
          1 TTTTATAT

       4057 ACACTTTTAT


Statistics
Matches: 80,  Mismatches: 9, Indels: 25
        0.70            0.08        0.22

Matches are distributed among these distances:
  16    1  0.01
  17   12  0.15
  18   30  0.38
  19   20  0.25
  20    9  0.11
  21    5  0.06
  22    3  0.04

ACGTcount: A:0.32, C:0.02, G:0.06, T:0.61


Consensus pattern (17 bp):   
TTTTATATTTTTTAATA

Found at i:4052 original size:20 final size:19

Alignment explanation


    Indices: 4002--4057  Score: 53
    Period size: 20  Copynumber: 2.9  Consensus size: 19

       3992 TATTTTGTAT

                   *         * 
       4002 TTTTTAATAA-TTTTATGA
          1 TTTTTAAGAATTTTTATAA

                                
       4020 TTTTTAATG-ATTTTTATAA
          1 TTTTTAA-GAATTTTTATAA

                          *    
       4039 GTTTTTAAGAATTTATATA
          1 -TTTTTAAGAATTTTTATA

       4058 CACTTTTATA


Statistics
Matches: 31,  Mismatches: 3, Indels: 6
        0.77            0.08        0.15

Matches are distributed among these distances:
  18    8  0.26
  19    8  0.26
  20   15  0.48

ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59


Consensus pattern (19 bp):   
TTTTTAAGAATTTTTATAA
Done.