Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013220.1 Kokia drynarioides strain JFW-HI SEQ_128239, 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: 8342
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.26

Warning! 330 characters in sequence are not A, C, G, or T


Found at i:630 original size:18 final size:18

Alignment explanation


    Indices: 588--630  Score: 50
    Period size: 18  Copynumber: 2.4  Consensus size: 18

        578 CAATAACTTT

                             *
        588 TACTAATATTAATAACAG
          1 TACTAATATTAATAACAA

             **            *  
        606 TTTTAATATTAATAATAA
          1 TACTAATATTAATAACAA

                   
        624 TACTAAT
          1 TACTAAT

        631 GACCCCATTA


Statistics
Matches: 19,  Mismatches: 6, Indels: 0
        0.76            0.24        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42


Consensus pattern (18 bp):   
TACTAATATTAATAACAA

Found at i:696 original size:3 final size:3

Alignment explanation


    Indices: 690--735  Score: 56
    Period size: 3  Copynumber: 14.3  Consensus size: 3

        680 AAATGTTTTG

                                    *                                   
        690 ATA ATA ATA ATA ATA ATA TTA ATA ATTA ATA ATTA ATA ATTA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA A-TA ATA A-TA ATA A

        736 AAAAAACACG


Statistics
Matches: 38,  Mismatches: 2, Indels: 6
        0.83            0.04        0.13

Matches are distributed among these distances:
   3   29  0.76
   4    9  0.24

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


Consensus pattern (3 bp):   
ATA

Found at i:719 original size:7 final size:7

Alignment explanation


    Indices: 691--735  Score: 69
    Period size: 7  Copynumber: 6.9  Consensus size: 7

        681 AATGTTTTGA

                   
        691 TAATAA-
          1 TAATAAT

                   
        697 TAATAA-
          1 TAATAAT

                   
        703 TAAT-AT
          1 TAATAAT

                   
        709 TAATAAT
          1 TAATAAT

                   
        716 TAATAAT
          1 TAATAAT

                   
        723 TAATAAT
          1 TAATAAT

                  
        730 TAATAA
          1 TAATAA

        736 AAAAAACACG


Statistics
Matches: 37,  Mismatches: 0, Indels: 3
        0.93            0.00        0.08

Matches are distributed among these distances:
   5    1  0.03
   6   14  0.38
   7   22  0.59

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


Consensus pattern (7 bp):   
TAATAAT

Found at i:2223 original size:59 final size:59

Alignment explanation


    Indices: 2071--2396  Score: 487
    Period size: 59  Copynumber: 5.6  Consensus size: 59

       2061 GAGGTCCCTA

                         *                                             
       2071 AACCTTCCAAAAAATACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTAACCCCG
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG

                                         *                *             
       2129 AACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAAATCCTATTTTTAACCCCG
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCC-AAAAATCCCATTTTTAACCCCG

                             *                      *               *  
       2189 AACCTTCCAAAAATTACTATTTTA-CCCCGAACTTCCAAAGATCCCATTTTTAACCTCG
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG

                                       *             *          *     *
       2247 AACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAGTCCCATTTTTTACCCCA
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG

                                                        *    *  *    * 
       2306 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTCTTGACCCTG
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG

                                    *        
       2365 AACCTTCC-AAAATTACCATTTTATCCCCGAAC
          1 AACCTTCCAAAAATTACCATTTTACCCCCGAAC

       2397 GTTTGAAATT


Statistics
Matches: 242,  Mismatches: 23, Indels: 6
        0.89            0.08        0.02

Matches are distributed among these distances:
  58  100  0.41
  59  108  0.45
  60   34  0.14

ACGTcount: A:0.34, C:0.34, G:0.04, T:0.29


Consensus pattern (59 bp):   
AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG

Done.