Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008401.1 Kokia drynarioides strain JFW-HI SEQ_123070, 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: 2099
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40


Found at i:154 original size:13 final size:13

Alignment explanation


    Indices: 131--163  Score: 52
    Period size: 13  Copynumber: 2.7  Consensus size: 13

        121 TTTATTTTAA

                         
        131 ATATA-TAATATT
          1 ATATATTAATATT

                         
        143 ATATATTAATATT
          1 ATATATTAATATT

                     
        156 ATAT-TTAA
          1 ATATATTAA

        164 GATATAGTCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  12    9  0.45
  13   11  0.55

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (13 bp):   
ATATATTAATATT

Found at i:296 original size:24 final size:25

Alignment explanation


    Indices: 246--304  Score: 68
    Period size: 24  Copynumber: 2.4  Consensus size: 25

        236 TATTTTATAT

                      *          *   
        246 ATTAAAATATTATTAATAAATTATA
          1 ATTAAAATATCATTAATAAATAATA

                                      
        271 ATTAAAATATCA-TAAT-AATAACTA
          1 ATTAAAATATCATTAATAAATAA-TA

               *      
        295 ATTTAAATAT
          1 ATTAAAATAT

        305 TATTTAAGTG


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  23    4  0.13
  24   15  0.50
  25   11  0.37

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


Consensus pattern (25 bp):   
ATTAAAATATCATTAATAAATAATA

Found at i:718 original size:23 final size:23

Alignment explanation


    Indices: 701--758  Score: 73
    Period size: 23  Copynumber: 2.5  Consensus size: 23

        691 TTAATGTTCA

                                   
        701 CGAACATGTTCATTTAATTTAAT
          1 CGAACATGTTCATTTAATTTAAT

                         **   *     
        724 CGAACATGTTCA-CGAACATTAAT
          1 CGAACATGTTCATTTAA-TTTAAT

                        
        747 CGAACATGTTCA
          1 CGAACATGTTCA

        759 GGGATATTAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  22    2  0.06
  23   29  0.94

ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33


Consensus pattern (23 bp):   
CGAACATGTTCATTTAATTTAAT

Found at i:767 original size:23 final size:23

Alignment explanation


    Indices: 719--811  Score: 105
    Period size: 23  Copynumber: 4.0  Consensus size: 23

        709 TTCATTTAAT

                                   
        719 TTAATCGAACATGTTCACGAACA
          1 TTAATCGAACATGTTCACGAACA

                             * * * 
        742 TTAATCGAACATGTTCAGGGATA
          1 TTAATCGAACATGTTCACGAACA

                *      *     *     
        765 TTAAACGAACACGTTCATGAACA
          1 TTAATCGAACATGTTCACGAACA

                  *     *           
        788 TATAATTGAACACGTTCACGAACA
          1 T-TAATCGAACATGTTCACGAACA

        812 ATATTAATGA


Statistics
Matches: 58,  Mismatches: 11, Indels: 1
        0.83            0.16        0.01

Matches are distributed among these distances:
  23   39  0.67
  24   19  0.33

ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26


Consensus pattern (23 bp):   
TTAATCGAACATGTTCACGAACA

Found at i:919 original size:12 final size:12

Alignment explanation


    Indices: 902--937  Score: 54
    Period size: 12  Copynumber: 3.0  Consensus size: 12

        892 GCATTGATAA

                        
        902 ATAAACGAGCTT
          1 ATAAACGAGCTT

                        
        914 ATAAACGAGCTT
          1 ATAAACGAGCTT

            *    *      
        926 TTAAATGAGCTT
          1 ATAAACGAGCTT

        938 GTTCGTGAAC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  12   22  1.00

ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31


Consensus pattern (12 bp):   
ATAAACGAGCTT

Found at i:1742 original size:24 final size:25

Alignment explanation


    Indices: 1692--1750  Score: 68
    Period size: 24  Copynumber: 2.4  Consensus size: 25

       1682 TATTTTATAT

                      *          *   
       1692 ATTAAAATATTATTAATAAATTATA
          1 ATTAAAATATCATTAATAAATAATA

                                      
       1717 ATTAAAATATCA-TAAT-AATAACTA
          1 ATTAAAATATCATTAATAAATAA-TA

               *      
       1741 ATTTAAATAT
          1 ATTAAAATAT

       1751 TATTTAAGTG


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  23    4  0.13
  24   15  0.50
  25   11  0.37

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


Consensus pattern (25 bp):   
ATTAAAATATCATTAATAAATAATA
Done.