Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001266.1 Kokia drynarioides strain JFW-HI SEQ_112644, 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: 22190
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38


Found at i:273 original size:19 final size:18

Alignment explanation


    Indices: 232--285  Score: 65
    Period size: 18  Copynumber: 2.9  Consensus size: 18

        222 CAAAAATTAC

                    * *       
        232 TTATTTAATATTATTTTT
          1 TTATTTAAAAATATTTTT

                              
        250 TTATTTAAAAATA-TTTT
          1 TTATTTAAAAATATTTTT

                               
        267 TTATATTAAAAATACTTTT
          1 TTAT-TTAAAAATA-TTTT

        286 AAAAAACATT


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  17    8  0.26
  18   20  0.65
  20    3  0.10

ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61


Consensus pattern (18 bp):   
TTATTTAAAAATATTTTT

Found at i:286 original size:17 final size:17

Alignment explanation


    Indices: 248--286  Score: 53
    Period size: 17  Copynumber: 2.3  Consensus size: 17

        238 AATATTATTT

                            *
        248 TTTTATTTAAAAATATT
          1 TTTTATTTAAAAATATC

                              
        265 TTTTATATTAAAAATA-C
          1 TTTTAT-TTAAAAATATC

                 
        282 TTTTA
          1 TTTTA

        287 AAAAACATTA


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

Matches are distributed among these distances:
  17   11  0.55
  18    9  0.45

ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56


Consensus pattern (17 bp):   
TTTTATTTAAAAATATC

Found at i:3212 original size:22 final size:24

Alignment explanation


    Indices: 3165--3216  Score: 72
    Period size: 22  Copynumber: 2.2  Consensus size: 24

       3155 TATAAACGTG

                                 *   
       3165 TAAATATATTTCAATTATGTATATA
          1 TAAATATATTT-AATTATGTAAATA

                                    
       3190 TAAATATATTT-A-TATGTAAATA
          1 TAAATATATTTAATTATGTAAATA

                 
       3212 TAAAT
          1 TAAAT

       3217 TTTAAAATAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  22   14  0.54
  23    1  0.04
  25   11  0.42

ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46


Consensus pattern (24 bp):   
TAAATATATTTAATTATGTAAATA

Found at i:6145 original size:38 final size:38

Alignment explanation


    Indices: 6092--6181  Score: 96
    Period size: 38  Copynumber: 2.4  Consensus size: 38

       6082 ATGATTTAAG

                       *                 *  *  *   
       6092 ATTAAAA-AAACATAATAA-CTCATGAATTAAGTATAAT
          1 ATTAAAATAAAAATAATAATCTC-TGAATAAAATAAAAT

                                *                 
       6129 ATTAAAATAAAAATAATAATTTCTGAATAAAATAAAAT
          1 ATTAAAATAAAAATAATAATCTCTGAATAAAATAAAAT

                            
       6167 -TTAAAAATAAAAATA
          1 ATT-AAAATAAAAATA

       6182 CATTTGATGA


Statistics
Matches: 45,  Mismatches: 5, Indels: 5
        0.82            0.09        0.09

Matches are distributed among these distances:
  37    9  0.20
  38   34  0.76
  39    2  0.04

ACGTcount: A:0.62, C:0.04, G:0.03, T:0.30


Consensus pattern (38 bp):   
ATTAAAATAAAAATAATAATCTCTGAATAAAATAAAAT

Found at i:6646 original size:29 final size:29

Alignment explanation


    Indices: 6614--6674  Score: 113
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       6604 AAAAAAAATC

                                     *   
       6614 AAAGAAGAGATATAGAGTTAAAATTTTAT
          1 AAAGAAGAGATATAGAGTTAAAATTGTAT

                                         
       6643 AAAGAAGAGATATAGAGTTAAAATTGTAT
          1 AAAGAAGAGATATAGAGTTAAAATTGTAT

               
       6672 AAA
          1 AAA

       6675 ATGTATACAC


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.54, C:0.00, G:0.18, T:0.28


Consensus pattern (29 bp):   
AAAGAAGAGATATAGAGTTAAAATTGTAT

Found at i:15489 original size:22 final size:22

Alignment explanation


    Indices: 15461--15511  Score: 93
    Period size: 22  Copynumber: 2.3  Consensus size: 22

      15451 ACATTGGGCT

                                  
      15461 TGTTGGTGCAACCATATGAAAA
          1 TGTTGGTGCAACCATATGAAAA

                        *         
      15483 TGTTGGTGCAACTATATGAAAA
          1 TGTTGGTGCAACCATATGAAAA

                   
      15505 TGTTGGT
          1 TGTTGGT

      15512 CCAAGTGTTC


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  22   28  1.00

ACGTcount: A:0.31, C:0.10, G:0.25, T:0.33


Consensus pattern (22 bp):   
TGTTGGTGCAACCATATGAAAA
Done.