Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004898.1 Kokia drynarioides strain JFW-HI SEQ_118589, 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: 2391
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33


Found at i:1548 original size:25 final size:25

Alignment explanation


    Indices: 1520--1594  Score: 65
    Period size: 25  Copynumber: 3.2  Consensus size: 25

       1510 TCCCCTCTAT

                                     
       1520 TAAAAAATAAACAAATCAATCCTTA
          1 TAAAAAATAAACAAATCAATCCTTA

                              * *     
       1545 T--AAAAT--AC-AA-C-TTTCTCTA
          1 TAAAAAATAAACAAATCAATCCT-TA

                                      
       1564 TTAAAAAATAAACAAATCAATCCTTA
          1 -TAAAAAATAAACAAATCAATCCTTA

                 
       1590 TAAAA
          1 TAAAA

       1595 TACAACTTTC


Statistics
Matches: 37,  Mismatches: 4, Indels: 18
        0.63            0.07        0.31

Matches are distributed among these distances:
  18    3  0.08
  19    3  0.08
  20    3  0.08
  21    2  0.05
  22    5  0.14
  23    5  0.14
  24    2  0.05
  25    8  0.22
  26    3  0.08
  27    3  0.08

ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28


Consensus pattern (25 bp):   
TAAAAAATAAACAAATCAATCCTTA

Found at i:1549 original size:24 final size:24

Alignment explanation


    Indices: 1522--1594  Score: 66
    Period size: 22  Copynumber: 3.2  Consensus size: 24

       1512 CCCTCTATTA

                                    
       1522 AAAAATAAACAAATCAATCCTTAT
          1 AAAAATAAACAAATCAATCCTTAT

                        **       *    
       1546 -AAAATACAAC-TTTC--TCTATTA-
          1 AAAAATA-AACAAATCAATC-CTTAT

                                    
       1567 AAAAATAAACAAATCAATCCTTAT
          1 AAAAATAAACAAATCAATCCTTAT

                
       1591 AAAA
          1 AAAA

       1595 TACAACTTTC


Statistics
Matches: 36,  Mismatches: 6, Indels: 14
        0.64            0.11        0.25

Matches are distributed among these distances:
  21    5  0.14
  22   11  0.31
  23   11  0.31
  24    9  0.25

ACGTcount: A:0.56, C:0.16, G:0.00, T:0.27


Consensus pattern (24 bp):   
AAAAATAAACAAATCAATCCTTAT

Found at i:1578 original size:45 final size:45

Alignment explanation


    Indices: 1514--1605  Score: 184
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       1504 ACTTTATCCC

                                                         
       1514 CTCTATTAAAAAATAAACAAATCAATCCTTATAAAATACAACTTT
          1 CTCTATTAAAAAATAAACAAATCAATCCTTATAAAATACAACTTT

                                                         
       1559 CTCTATTAAAAAATAAACAAATCAATCCTTATAAAATACAACTTT
          1 CTCTATTAAAAAATAAACAAATCAATCCTTATAAAATACAACTTT

              
       1604 CT
          1 CT

       1606 GATCATTTTA


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   47  1.00

ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32


Consensus pattern (45 bp):   
CTCTATTAAAAAATAAACAAATCAATCCTTATAAAATACAACTTT
Done.