Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004547.1 Kokia drynarioides strain JFW-HI SEQ_118014, 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: 17749
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:37 original size:18 final size:18

Alignment explanation


    Indices: 11--45  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

          1 TAAATAATAA

                *       *     
         11 AATATTATTATTTATTAT
          1 AATAATATTATTAATTAT

                             
         29 AATAATATTATTAATTA
          1 AATAATATTATTAATTA

         46 ATATATCATT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (18 bp):   
AATAATATTATTAATTAT

Found at i:37 original size:21 final size:20

Alignment explanation


    Indices: 7--50  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 20

          1 TAAATA

                          *   * 
          7 ATAAAATATTATTATTTATT
          1 ATAAAATATTATTAATTAAT

                                 
         27 ATAATAATATTATTAATTAAT
          1 ATAA-AATATTATTAATTAAT

               
         48 ATA
          1 ATA

         51 TCATTTGAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20    4  0.19
  21   17  0.81

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (20 bp):   
ATAAAATATTATTAATTAAT

Found at i:3744 original size:18 final size:18

Alignment explanation


    Indices: 3718--3752  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3708 TAAATAATAA

                *       *     
       3718 AATATTATTATTTATTAT
          1 AATAATATTATTAATTAT

                             
       3736 AATAATATTATTAATTA
          1 AATAATATTATTAATTA

       3753 ATATATCATT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (18 bp):   
AATAATATTATTAATTAT

Found at i:3744 original size:21 final size:20

Alignment explanation


    Indices: 3714--3757  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       3704 AATATAAATA

                          *   * 
       3714 ATAAAATATTATTATTTATT
          1 ATAAAATATTATTAATTAAT

                                 
       3734 ATAATAATATTATTAATTAAT
          1 ATAA-AATATTATTAATTAAT

               
       3755 ATA
          1 ATA

       3758 TCATTTGAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20    4  0.19
  21   17  0.81

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (20 bp):   
ATAAAATATTATTAATTAAT

Found at i:9921 original size:21 final size:21

Alignment explanation


    Indices: 9897--9936  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       9887 TACCTTGTAC

                     *   *       
       9897 TTCTACCGATACATGTAAGAG
          1 TTCTACCGAAACAAGTAAGAG

                               
       9918 TTCTACCGAAACAAGTAAG
          1 TTCTACCGAAACAAGTAAG

       9937 CATAATTCAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25


Consensus pattern (21 bp):   
TTCTACCGAAACAAGTAAGAG

Found at i:10490 original size:43 final size:42

Alignment explanation


    Indices: 10380--10517  Score: 152
    Period size: 43  Copynumber: 3.2  Consensus size: 42

      10370 CCGATTTGTA

                            *  *      *    *    *       
      10380 AGTCTTCCTTTAAAACGTATTCTCATACTC-ATCTCGAGTCACG
          1 AGTCTTCC-TTAAAACATAATCTCATGCTCTTTC-CAAGTCACG

                                                      
      10423 AGTCTTCCTTAAAACATAATCTCATGCTCTTTCCAAGTCACG
          1 AGTCTTCCTTAAAACATAATCTCATGCTCTTTCCAAGTCACG

                    *  *                      *   *  * 
      10465 AGTCTTCTTTTTAAACATAATCTCATGCTCTTTCTAAGACATG
          1 AGTCTTC-CTTAAAACATAATCTCATGCTCTTTCCAAGTCACG

                      
      10508 AGTCTTCCTT
          1 AGTCTTCCTT

      10518 TAATATACTC


Statistics
Matches: 82,  Mismatches: 11, Indels: 5
        0.84            0.11        0.05

Matches are distributed among these distances:
  42   35  0.43
  43   47  0.57

ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38


Consensus pattern (42 bp):   
AGTCTTCCTTAAAACATAATCTCATGCTCTTTCCAAGTCACG

Found at i:10546 original size:41 final size:41

Alignment explanation


    Indices: 10501--10645  Score: 202
    Period size: 41  Copynumber: 3.5  Consensus size: 41

      10491 GCTCTTTCTA

                                                  *  
      10501 AGACATGAGTCTTCCTTTAATATACTCTCATGTTCATCTCG
          1 AGACATGAGTCTTCCTTTAATATACTCTCATGTTCATCCCG

                         *         *  *               
      10542 AGACATGAGTCTTTCTTTAATATGCTTTCATGCTT-ATCCCG
          1 AGACATGAGTCTTCCTTTAATATACTCTCATG-TTCATCCCG

            *                               *        
      10583 TGACATGAGTCTTCCTTTAATATACTCTCATGCTCATCCCG
          1 AGACATGAGTCTTCCTTTAATATACTCTCATGTTCATCCCG

                     **           
      10624 AGACATGAGAATTCCTTTAATA
          1 AGACATGAGTCTTCCTTTAATA

      10646 CATCAAGTGA


Statistics
Matches: 90,  Mismatches: 12, Indels: 4
        0.85            0.11        0.04

Matches are distributed among these distances:
  40    1  0.01
  41   87  0.97
  42    2  0.02

ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38


Consensus pattern (41 bp):   
AGACATGAGTCTTCCTTTAATATACTCTCATGTTCATCCCG
Done.