Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001793.1 Kokia drynarioides strain JFW-HI SEQ_113526, 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: 5448
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33


Found at i:1823 original size:29 final size:30

Alignment explanation


    Indices: 1798--1853  Score: 89
    Period size: 28  Copynumber: 1.9  Consensus size: 30

       1788 GAAAATTCAT

                               *          
       1798 AAAAAAAAAAT-CAAATATTA-CAAATTGC
          1 AAAAAAAAAATCCAAATATAATCAAATTGC

                                        
       1826 AAAAAAAAAATCCAAATATAATCAAATT
          1 AAAAAAAAAATCCAAATATAATCAAATT

       1854 AAAAAGCCTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  28   11  0.44
  29    8  0.32
  30    6  0.24

ACGTcount: A:0.66, C:0.11, G:0.02, T:0.21


Consensus pattern (30 bp):   
AAAAAAAAAATCCAAATATAATCAAATTGC

Found at i:1858 original size:29 final size:28

Alignment explanation


    Indices: 1798--1858  Score: 79
    Period size: 29  Copynumber: 2.1  Consensus size: 28

       1788 GAAAATTCAT

                              *        *
       1798 AAAAAAAAAATCAAATATTACAAATTGC
          1 AAAAAAAAAATCAAATATAACAAATTGA

                                          
       1826 AAAAAAAAAATCCAAATATAATCAAATT-A
          1 AAAAAAAAAAT-CAAATATAA-CAAATTGA

                
       1855 AAAA
          1 AAAA

       1859 GCCTTATAAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  28   11  0.38
  29   12  0.41
  30    6  0.21

ACGTcount: A:0.69, C:0.10, G:0.02, T:0.20


Consensus pattern (28 bp):   
AAAAAAAAAATCAAATATAACAAATTGA

Found at i:2506 original size:15 final size:15

Alignment explanation


    Indices: 2486--2520  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       2476 AAATTAGAAG

                           
       2486 AAAAACAAAATATAA
          1 AAAAACAAAATATAA

                  **       
       2501 AAAAACTGAATATAA
          1 AAAAACAAAATATAA

                 
       2516 AAAAA
          1 AAAAA

       2521 GAAAGAGACA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14


Consensus pattern (15 bp):   
AAAAACAAAATATAA

Found at i:3993 original size:30 final size:30

Alignment explanation


    Indices: 3930--3993  Score: 78
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       3920 TTTTTTAGTT

                                      *   
       3930 AATTTAACTTTTAATATTTAAAAAGAGTCA
          1 AATTTAACTTTTAATATTTAAAAAGAATCA

                                          * 
       3960 AATTTAA-TTATTAATATTTCAAAAA-AATTA
          1 AATTTAACTT-TTAATATTT-AAAAAGAATCA

                
       3990 AATT
          1 AATT

       3994 GTTGTTTTTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  29    2  0.07
  30   23  0.77
  31    5  0.17

ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42


Consensus pattern (30 bp):   
AATTTAACTTTTAATATTTAAAAAGAATCA

Found at i:4315 original size:16 final size:15

Alignment explanation


    Indices: 4266--4316  Score: 50
    Period size: 16  Copynumber: 3.3  Consensus size: 15

       4256 TAATTAAAAA

                           
       4266 ATTAAGGATTAAATT
          1 ATTAAGGATTAAATT

                  *        * 
       4281 ATTAA-AATATATAAAT
          1 ATTAAGGAT-TA-AATT

                            
       4297 ATTAAGGATTAAATTT
          1 ATTAAGGATTAAA-TT

                
       4313 ATTA
          1 ATTA

       4317 TTACTTCTTA


Statistics
Matches: 28,  Mismatches: 4, Indels: 7
        0.72            0.10        0.18

Matches are distributed among these distances:
  14    2  0.07
  15    9  0.32
  16   15  0.54
  17    2  0.07

ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41


Consensus pattern (15 bp):   
ATTAAGGATTAAATT
Done.