Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012172.1 Kokia drynarioides strain JFW-HI SEQ_127173, 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: 11848
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:10519 original size:30 final size:28

Alignment explanation


    Indices: 10483--10704  Score: 198
    Period size: 30  Copynumber: 7.4  Consensus size: 28

      10473 AAAAGGGTAA

                                          
      10483 TTTTGGAAGTTTCGGGGTCAAAAATGTGAT
          1 TTTTGGAAGTTTCGGGGT-AAAAATG-GAT

                   *  *              *      
      10513 TTTTGGATG-CTCGAGGGTTAAAAACGGTAAT
          1 TTTTGGAAGTTTCG-GGG-TAAAAATGG--AT

                        *               * 
      10544 TTTTGGAAGTTTTGGGGTTAAAAATGGGTT
          1 TTTTGGAAGTTTCGGGG-TAAAAAT-GGAT

                                          
      10574 TTTTGGAAGTTT-GAGGGTAAAAATGGAAT
          1 TTTTGGAAGTTTCG-GGGTAAAAATGG-AT

                          *               
      10603 TTTTGGAAGTTTCGAGGTCAAAAATGGAAT
          1 TTTTGGAAGTTTCGGGGT-AAAAATGG-AT

                          *               
      10633 TTTTGGAAGTTTCGAGGTAAAAAATGGGAT
          1 TTTTGGAAGTTTCGGGGT-AAAAAT-GGAT

             *                            
      10663 TATTGGAAG-TTCGAGGGTAAAAATGGAAT
          1 TTTTGGAAGTTTCG-GGGTAAAAATGG-AT

                         
      10692 TTTTGGACAGTTT
          1 TTTTGGA-AGTTT

      10705 AGGGACCTCC


Statistics
Matches: 163,  Mismatches: 14, Indels: 29
        0.79            0.07        0.14

Matches are distributed among these distances:
  28    4  0.02
  29   46  0.28
  30   84  0.52
  31   25  0.15
  32    4  0.02

ACGTcount: A:0.30, C:0.05, G:0.30, T:0.36


Consensus pattern (28 bp):   
TTTTGGAAGTTTCGGGGTAAAAATGGAT

Found at i:10627 original size:59 final size:59

Alignment explanation


    Indices: 10483--10708  Score: 246
    Period size: 59  Copynumber: 3.8  Consensus size: 59

      10473 AAAAGGGTAA

                          *                       * * *            *      
      10483 TTTTGGAAGTTTCGGGGTCAAAAATGTG-ATTTTTGGATGCTCGAGGGTTAAAAACGGTAAT
          1 TTTTGGAAGTTTCGAGGTCAAAAATG-GAATTTTTGGAAGTTTGAGGG-TAAAAATGG-AAT

                        * *   *        **                              
      10544 TTTTGGAAGTTTTGGGGTTAAAAATGGGTTTTTTGGAAGTTTGAGGGTAAAAATGGAAT
          1 TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAAT

                                                                      *  
      10603 TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTCGA-GGTAAAAAATGGGAT
          1 TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTT-GAGGGT-AAAAATGGAAT

             *                                               
      10663 TATTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGACAGTTT-AGGG
          1 TTTTGGAAGTTTCGA-GGTCAAAAATGGAATTTTTGGA-AGTTTGAGGG

      10709 ACCTCCGAGG


Statistics
Matches: 145,  Mismatches: 14, Indels: 14
        0.84            0.08        0.08

Matches are distributed among these distances:
  58    1  0.01
  59   68  0.47
  60   37  0.26
  61   39  0.27

ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35


Consensus pattern (59 bp):   
TTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAAT

Found at i:10657 original size:89 final size:91

Alignment explanation


    Indices: 10483--10704  Score: 283
    Period size: 89  Copynumber: 2.5  Consensus size: 91

      10473 AAAAGGGTAA

                                                   *  *        *             
      10483 TTTTGGAAGTTTCG-GGGTCAAAAATGTG-ATTTTTGGATG-CTCGAGGGTTAAAAACGGTAATT
          1 TTTTGGAAGTTT-GAGGGT-AAAAATG-GAATTTTTGGAAGTTTCGAGGGTCAAAAACGGTAATT

                       * *   *         * 
      10545 TTTGGAAGTTTTGGGGTTAAAAATGGGTT
         63 TTTGGAAGTTTCGAGGTAAAAAATGGGAT

                                                                  *          
      10574 TTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGA-GGTCAAAAATGG-AATTTTT
          1 TTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTCAAAAACGGTAATTTTT

                                      
      10637 GGAAGTTTCGAGGTAAAAAATGGGAT
         66 GGAAGTTTCGAGGTAAAAAATGGGAT

             *         *                              
      10663 TATTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGACAGTTT
          1 TTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGA-AGTTT

      10705 AGGGACCTCC


Statistics
Matches: 117,  Mismatches: 10, Indels: 9
        0.86            0.07        0.07

Matches are distributed among these distances:
  89   64  0.55
  90   33  0.28
  91   20  0.17

ACGTcount: A:0.30, C:0.05, G:0.30, T:0.36


Consensus pattern (91 bp):   
TTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGGTCAAAAACGGTAATTTTT
GGAAGTTTCGAGGTAAAAAATGGGAT

Found at i:11838 original size:3 final size:3

Alignment explanation


    Indices: 11792--11820  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

      11782 TCATTAATGC

                                                  
      11792 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA

      11821 AAACAGTTAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
TAT

Done.