Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002492.1 Kokia drynarioides strain JFW-HI SEQ_114646, 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: 18152
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:4290 original size:25 final size:25

Alignment explanation


    Indices: 4260--4309  Score: 73
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       4250 TGCTTACTGG

                  *      *           
       4260 TTCAGTGCAAGAGTAGCCACAACAA
          1 TTCAGTACAAGAGCAGCCACAACAA

                    *                
       4285 TTCAGTACGAGAGCAGCCACAACAA
          1 TTCAGTACAAGAGCAGCCACAACAA

       4310 AGAAGAAAAA


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.40, C:0.26, G:0.20, T:0.14


Consensus pattern (25 bp):   
TTCAGTACAAGAGCAGCCACAACAA

Found at i:4563 original size:39 final size:41

Alignment explanation


    Indices: 4491--4571  Score: 121
    Period size: 39  Copynumber: 2.0  Consensus size: 41

       4481 AAAAGAAGTT

                              *                       
       4491 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTA
          1 GTTTATGAG-GTTATTTAAGAATAAAATTATATTTGGGTTTA

                                  *                  
       4533 GTTTATGA-GTT-TTTAAGAATGAAATTATATTTGGGTTTA
          1 GTTTATGAGGTTATTTAAGAATAAAATTATATTTGGGTTTA

       4572 AAAATATTTG


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  39   26  0.70
  40    3  0.08
  42    8  0.22

ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48


Consensus pattern (41 bp):   
GTTTATGAGGTTATTTAAGAATAAAATTATATTTGGGTTTA

Found at i:11647 original size:18 final size:18

Alignment explanation


    Indices: 11624--11658  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      11614 CAGATATGTG

                              
      11624 TTTGACATGCAAAAAGGT
          1 TTTGACATGCAAAAAGGT

                  *          
      11642 TTTGACGTGCAAAAAGG
          1 TTTGACATGCAAAAAGG

      11659 AGCCGAAAGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26


Consensus pattern (18 bp):   
TTTGACATGCAAAAAGGT

Found at i:13237 original size:51 final size:51

Alignment explanation


    Indices: 13178--13420  Score: 369
    Period size: 51  Copynumber: 4.8  Consensus size: 51

      13168 CTATAAACGA

                                                          *    
      13178 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATAGATT
          1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT

                                                               
      13229 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
          1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT

                   *                                     *     
      13280 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
          1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT

                   *         *      *                * * * *   
      13331 AAAGGTCTGATGACTAATTGTCATTGTGAGTAAATGAATCCATGACGAATT
          1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT

                           *         *      *      
      13382 AAAGGTCCGATGACTCAGTGTCATCATGAGTATATGAAT
          1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT

      13421 TTCTATACGG


Statistics
Matches: 178,  Mismatches: 14, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  51  178  1.00

ACGTcount: A:0.33, C:0.14, G:0.23, T:0.31


Consensus pattern (51 bp):   
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT

Done.