Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007755.1 Kokia drynarioides strain JFW-HI SEQ_122388, 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: 29538
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:1902 original size:22 final size:22

Alignment explanation


    Indices: 1877--1919  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1867 GTACTAAAAA

                  *               
       1877 ATAAAATATTCTTCCAAAATAT
          1 ATAAAAAATTCTTCCAAAATAT

                          *      
       1899 ATAAAAAATTCTTCTAAAATA
          1 ATAAAAAATTCTTCCAAAATA

       1920 CGCATATAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35


Consensus pattern (22 bp):   
ATAAAAAATTCTTCCAAAATAT

Found at i:7657 original size:29 final size:29

Alignment explanation


    Indices: 7615--7675  Score: 113
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       7605 GGCTACCACA

                                         
       7615 AGACTTGCATTTCCTCACATGTTTAACTG
          1 AGACTTGCATTTCCTCACATGTTTAACTG

                   *                     
       7644 AGACTTGTATTTCCTCACATGTTTAACTG
          1 AGACTTGCATTTCCTCACATGTTTAACTG

               
       7673 AGA
          1 AGA

       7676 TGCAAATCAA


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:0.26, C:0.21, G:0.15, T:0.38


Consensus pattern (29 bp):   
AGACTTGCATTTCCTCACATGTTTAACTG

Found at i:10666 original size:16 final size:16

Alignment explanation


    Indices: 10629--10670  Score: 50
    Period size: 15  Copynumber: 2.7  Consensus size: 16

      10619 TGGCCAGACC

                  *  *      
      10629 TATTTTAATTTTATAA
          1 TATTTTTATATTATAA

                           *
      10645 TA-TTTTATATTATAT
          1 TATTTTTATATTATAA

                       
      10660 TATTTTTATAT
          1 TATTTTTATAT

      10671 ATTATGTAAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  15   12  0.55
  16   10  0.45

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (16 bp):   
TATTTTTATATTATAA

Found at i:10805 original size:28 final size:26

Alignment explanation


    Indices: 10760--10819  Score: 68
    Period size: 28  Copynumber: 2.2  Consensus size: 26

      10750 TAATATGACT

                         *             
      10760 ATATAAAAAATTTCAATAAGTAAAA-A
          1 ATATAAAAAATTTAAAT-AGTAAAATA

                                *       
      10786 ATATAAAAAATTATTAAATATTAAAATA
          1 ATATAAAAAA-T-TTAAATAGTAAAATA

                  
      10814 ATATAA
          1 ATATAA

      10820 TATAAATATT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  26   10  0.34
  27    7  0.24
  28   12  0.41

ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32


Consensus pattern (26 bp):   
ATATAAAAAATTTAAATAGTAAAATA

Found at i:15010 original size:19 final size:17

Alignment explanation


    Indices: 14960--15014  Score: 56
    Period size: 18  Copynumber: 3.1  Consensus size: 17

      14950 ATCCTATACC

                *       *    
      14960 AAAATTTTTAAATAATA
          1 AAAAATTTTAAAGAATA

                *              
      14977 CAAATATTTTAAAGAGATA
          1 -AAAAATTTTAAAGA-ATA

                              
      14996 AAAAATTTCTAAAGAATA
          1 AAAAATTT-TAAAGAATA

             
      15014 A
          1 A

      15015 CCAAAATTAG


Statistics
Matches: 31,  Mismatches: 4, Indels: 4
        0.79            0.10        0.10

Matches are distributed among these distances:
  18   22  0.71
  19    9  0.29

ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33


Consensus pattern (17 bp):   
AAAAATTTTAAAGAATA

Found at i:15303 original size:28 final size:28

Alignment explanation


    Indices: 15267--15331  Score: 78
    Period size: 28  Copynumber: 2.3  Consensus size: 28

      15257 AATCAGCAAA

                        *      *         
      15267 GATAAAATTTCATTTTAA-TTTTTAAAAT
          1 GATAAAATTT-AATTTAACGTTTTAAAAT

                *                       
      15295 GATATAATTTAATTTAACGTTTTAAAAT
          1 GATAAAATTTAATTTAACGTTTTAAAAT

            *        
      15323 TATAAAATT
          1 GATAAAATT

      15332 ATAAAAATAT


Statistics
Matches: 31,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  27    6  0.19
  28   25  0.81

ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48


Consensus pattern (28 bp):   
GATAAAATTTAATTTAACGTTTTAAAAT

Found at i:23236 original size:16 final size:16

Alignment explanation


    Indices: 23190--23236  Score: 51
    Period size: 16  Copynumber: 2.9  Consensus size: 16

      23180 TTAAATTATT

                             
      23190 TATATTGTTTTATTTTA
          1 TATATT-TTTTATTTTA

                    * *      
      23207 -ATATTTAATAATTTTA
          1 TATATTT-TTTATTTTA

                          
      23223 TATATTTTTTATTT
          1 TATATTTTTTATTT

      23237 ATTAAAATTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 5
        0.73            0.12        0.15

Matches are distributed among these distances:
  15    1  0.04
  16   17  0.71
  17    6  0.25

ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68


Consensus pattern (16 bp):   
TATATTTTTTATTTTA
Done.