Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008775.1 Kokia drynarioides strain JFW-HI SEQ_123458, 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: 12421
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:362 original size:20 final size:19

Alignment explanation


    Indices: 324--365  Score: 57
    Period size: 19  Copynumber: 2.2  Consensus size: 19

        314 ATATTTAAAA

                     *    *    
        324 AAAAATATTTAATATATTC
          1 AAAAATATTAAATAAATTC

                                
        343 AAAAATATTAAATAAAATTC
          1 AAAAATATTAAAT-AAATTC

               
        363 AAA
          1 AAA

        366 TATGAAACAC


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

Matches are distributed among these distances:
  19   12  0.60
  20    8  0.40

ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33


Consensus pattern (19 bp):   
AAAAATATTAAATAAATTC

Found at i:3506 original size:63 final size:63

Alignment explanation


    Indices: 3421--3547  Score: 227
    Period size: 63  Copynumber: 2.0  Consensus size: 63

       3411 TGTCATATGC

                          *                                                
       3421 GGGAGCCAATATTGCCATTTGAACTCAACAAAGGTTCATTTCGTCAACAACCATAATATCACT
          1 GGGAGCCAATATTGACATTTGAACTCAACAAAGGTTCATTTCGTCAACAACCATAATATCACT

                                           *                       *       
       3484 GGGAGCCAATATTGACATTTGAACTCAACAATGGTTCATTTCGTCAACAACCATATTATCACT
          1 GGGAGCCAATATTGACATTTGAACTCAACAAAGGTTCATTTCGTCAACAACCATAATATCACT

             
       3547 G
          1 G

       3548 CCACAATACA


Statistics
Matches: 61,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  63   61  1.00

ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28


Consensus pattern (63 bp):   
GGGAGCCAATATTGACATTTGAACTCAACAAAGGTTCATTTCGTCAACAACCATAATATCACT

Found at i:7899 original size:20 final size:19

Alignment explanation


    Indices: 7859--7899  Score: 55
    Period size: 20  Copynumber: 2.1  Consensus size: 19

       7849 TCTCAAGTTT

                          * *  
       7859 ATTTTATTTTATTATTCTA
          1 ATTTTATTTTATTACTATA

                                
       7878 ATTTTAATTTTATTACTATA
          1 ATTTT-ATTTTATTACTATA

              
       7898 AT
          1 AT

       7900 ATTTTATATT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  19    5  0.26
  20   14  0.74

ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63


Consensus pattern (19 bp):   
ATTTTATTTTATTACTATA

Found at i:7917 original size:18 final size:18

Alignment explanation


    Indices: 7868--7918  Score: 50
    Period size: 21  Copynumber: 2.7  Consensus size: 18

       7858 TATTTTATTT

                              
       7868 TATTATTCTAAT-TTTAA
          1 TATTATTCTAATATTTAA

             *                 * 
       7885 TTTTATTACTATAATATTTTA
          1 TATTATT-C--TAATATTTAA

                         
       7906 TATTATTCTAATA
          1 TATTATTCTAATA

       7919 AATTTAGATA


Statistics
Matches: 27,  Mismatches: 3, Indels: 7
        0.73            0.08        0.19

Matches are distributed among these distances:
  17    6  0.22
  18    6  0.22
  20    5  0.19
  21   10  0.37

ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59


Consensus pattern (18 bp):   
TATTATTCTAATATTTAA

Found at i:7919 original size:21 final size:21

Alignment explanation


    Indices: 7877--7923  Score: 53
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       7867 TTATTATTCT

                     *           
       7877 AATTTTAATTTTATTACTATA
          1 AATTTTAATATTATTACTATA

                                   
       7898 ATATTTT-ATATTATT-CTAATA
          1 A-ATTTTAATATTATTACT-ATA

                 
       7919 AATTT
          1 AATTT

       7924 AGATAAAAGT


Statistics
Matches: 23,  Mismatches: 1, Indels: 5
        0.79            0.03        0.17

Matches are distributed among these distances:
  20    6  0.26
  21   12  0.52
  22    5  0.22

ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57


Consensus pattern (21 bp):   
AATTTTAATATTATTACTATA
Done.