Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014982.1 Kokia drynarioides strain JFW-HI SEQ_130026, 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: 26147
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34

Warning! 210 characters in sequence are not A, C, G, or T


Found at i:3155 original size:24 final size:24

Alignment explanation


    Indices: 3116--3167  Score: 68
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       3106 TTTAGAGTAG

                    *  *            
       3116 TTTTTTATTATTATTTAAAATGAT
          1 TTTTTTATAATAATTTAAAATGAT

                            *    *  
       3140 TTTTTTATAATAATTTTAAATTAT
          1 TTTTTTATAATAATTTAAAATGAT

                
       3164 TTTT
          1 TTTT

       3168 ATAATTGTCA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65


Consensus pattern (24 bp):   
TTTTTTATAATAATTTAAAATGAT

Found at i:3324 original size:18 final size:17

Alignment explanation


    Indices: 3285--3320  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       3275 AATTTTTTAT

                             
       3285 ATTA-TAAAAATAAAAA
          1 ATTATTAAAAATAAAAA

                          *  
       3301 ATTATTAAAAATAAGAA
          1 ATTATTAAAAATAAAAA

               
       3318 ATT
          1 ATT

       3321 TATTCGGTTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  16    4  0.22
  17   14  0.78

ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31


Consensus pattern (17 bp):   
ATTATTAAAAATAAAAA

Found at i:4783 original size:27 final size:27

Alignment explanation


    Indices: 4743--4804  Score: 88
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       4733 TAAGGGTGTA

                   * *    *            
       4743 AGATCGGGATCTGATGTGGTGGATATT
          1 AGATCGGAAACTGAAGTGGTGGATATT

                                       
       4770 AGATCGGAAACTGAAGTGGTGGATATT
          1 AGATCGGAAACTGAAGTGGTGGATATT

             *      
       4797 AAATCGGA
          1 AGATCGGA

       4805 CGATGTCGGA


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   31  1.00

ACGTcount: A:0.31, C:0.08, G:0.34, T:0.27


Consensus pattern (27 bp):   
AGATCGGAAACTGAAGTGGTGGATATT

Found at i:5759 original size:30 final size:31

Alignment explanation


    Indices: 5725--5783  Score: 75
    Period size: 30  Copynumber: 1.9  Consensus size: 31

       5715 AGTTTTAATA

                    *  *                   
       5725 AATTTATATAACTTTCATAAT-TTTTTATTT
          1 AATTTATAAAAATTTCATAATGTTTTTATTT

                 *         *             
       5755 AATTTTTAAAAATTTTATAATGTTTTTAT
          1 AATTTATAAAAATTTCATAATGTTTTTAT

       5784 AATCCTTTCA


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  30   17  0.71
  31    7  0.29

ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59


Consensus pattern (31 bp):   
AATTTATAAAAATTTCATAATGTTTTTATTT

Found at i:20630 original size:24 final size:24

Alignment explanation


    Indices: 20596--20646  Score: 66
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      20586 TGACAATTAT

                            *  *    
      20596 AAAAATAATTTAAAATTATTATAA
          1 AAAAATAATTTAAAATAATAATAA

                  *    *            
      20620 AAAAATCATTTTAAATAATAATAA
          1 AAAAATAATTTAAAATAATAATAA

               
      20644 AAA
          1 AAA

      20647 CCTATTCTAA


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33


Consensus pattern (24 bp):   
AAAAATAATTTAAAATAATAATAA
Done.