Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013776.1 Kokia drynarioides strain JFW-HI SEQ_128804, 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: 5607
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.37


Found at i:59 original size:15 final size:16

Alignment explanation


    Indices: 38--73  Score: 56
    Period size: 15  Copynumber: 2.3  Consensus size: 16

         28 AATTTTATTT

                            
         38 TAATAATAAATTTAAA
          1 TAATAATAAATTTAAA

                     *      
         54 -AATAATAATTTTAAA
          1 TAATAATAAATTTAAA

                 
         69 TAATA
          1 TAATA

         74 TACTTCACAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  15   14  0.78
  16    4  0.22

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (16 bp):   
TAATAATAAATTTAAA

Found at i:1307 original size:21 final size:21

Alignment explanation


    Indices: 1269--1308  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1259 TCTTTTACCC

                                 
       1269 CCAAACAAAATTTAAAATCAT
          1 CCAAACAAAATTTAAAATCAT

                          *     
       1290 CCAAA-AAAATCTTTAAATC
          1 CCAAACAAAAT-TTAAAATC

       1309 TAAATAGTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    5  0.29
  21   12  0.71

ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25


Consensus pattern (21 bp):   
CCAAACAAAATTTAAAATCAT

Found at i:2304 original size:32 final size:32

Alignment explanation


    Indices: 2268--2332  Score: 103
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       2258 TAATTATTGT

                 *                          
       2268 GATGATAGATATCATTTTAATAAGGAATAAAA
          1 GATGACAGATATCATTTTAATAAGGAATAAAA

                         *     *            
       2300 GATGACAGATATCGTTTTATTAAGGAATAAAA
          1 GATGACAGATATCATTTTAATAAGGAATAAAA

             
       2332 G
          1 G

       2333 TATTAGTAAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  32   30  1.00

ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31


Consensus pattern (32 bp):   
GATGACAGATATCATTTTAATAAGGAATAAAA

Found at i:2376 original size:21 final size:21

Alignment explanation


    Indices: 2352--2402  Score: 59
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       2342 TTTTTTTTAT

                         *     * 
       2352 TTAATTAATAATTTAAAGTGA
          1 TTAATTAATAATTAAAAGTAA

                             *   
       2373 TTAATTAA-AATTAAAATTAA
          1 TTAATTAATAATTAAAAGTAA

                      
       2393 TTAAATTAAT
          1 TT-AATTAAT

       2403 TAACTAAAGA


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  20   11  0.44
  21   14  0.56

ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43


Consensus pattern (21 bp):   
TTAATTAATAATTAAAAGTAA

Found at i:2393 original size:16 final size:15

Alignment explanation


    Indices: 2372--2401  Score: 51
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       2362 ATTTAAAGTG

                            
       2372 ATTAATTAAAATTAAA
          1 ATTAATT-AAATTAAA

                          
       2388 ATTAATTAAATTAA
          1 ATTAATTAAATTAA

       2402 TTAACTAAAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    7  0.50
  16    7  0.50

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (15 bp):   
ATTAATTAAATTAAA

Found at i:3693 original size:23 final size:23

Alignment explanation


    Indices: 3667--3721  Score: 58
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       3657 TATTTCTTTG

                                    
       3667 ATTAATTGAGAAATTGAAT-TCTA
          1 ATTAATT-AGAAATTGAATCTCTA

                 *   * *            
       3690 ATTACCTTATACATTGAATCTCTA
          1 ATTA-ATTAGAAATTGAATCTCTA

                    
       3714 ATTAATTA
          1 ATTAATTA

       3722 TATAAATGAT


Statistics
Matches: 26,  Mismatches: 4, Indels: 4
        0.76            0.12        0.12

Matches are distributed among these distances:
  23   16  0.62
  24   10  0.38

ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42


Consensus pattern (23 bp):   
ATTAATTAGAAATTGAATCTCTA

Found at i:3722 original size:23 final size:23

Alignment explanation


    Indices: 3679--3723  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3669 TAATTGAGAA

                            *      
       3679 ATTGAATTCTAATTACCTTATAC
          1 ATTGAATTCTAATTACATTATAC

                                   
       3702 ATTGAATCTCTAATTA-ATTATA
          1 ATTGAAT-TCTAATTACATTATA

       3724 TAAATGATCT


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

Matches are distributed among these distances:
  23   12  0.60
  24    8  0.40

ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44


Consensus pattern (23 bp):   
ATTGAATTCTAATTACATTATAC
Done.