Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009244.1 Kokia drynarioides strain JFW-HI SEQ_123949, 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: 22761
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32

Warning! 25 characters in sequence are not A, C, G, or T


Found at i:4588 original size:43 final size:43

Alignment explanation


    Indices: 4527--4613  Score: 174
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       4517 CGACCGTTAT

                                                       
       4527 TATTTCGGTAATCTATGTTCATCGTTGGTTGCACTACTAGTAA
          1 TATTTCGGTAATCTATGTTCATCGTTGGTTGCACTACTAGTAA

                                                       
       4570 TATTTCGGTAATCTATGTTCATCGTTGGTTGCACTACTAGTAA
          1 TATTTCGGTAATCTATGTTCATCGTTGGTTGCACTACTAGTAA

             
       4613 T
          1 T

       4614 GCTGTAATAA


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  43   44  1.00

ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43


Consensus pattern (43 bp):   
TATTTCGGTAATCTATGTTCATCGTTGGTTGCACTACTAGTAA

Found at i:5884 original size:26 final size:25

Alignment explanation


    Indices: 5831--5884  Score: 63
    Period size: 26  Copynumber: 2.1  Consensus size: 25

       5821 AACATTTTTT

                         **     *    
       5831 TTTTTTAAATTAAGTTTACATAAGG
          1 TTTTTTAAATTAAAATTACAAAAGG

                                    * 
       5856 TTTTTTATAATTAAAATTACAAAATG
          1 TTTTTTA-AATTAAAATTACAAAAGG

               
       5882 TTT
          1 TTT

       5885 GCATCGTGAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  25    7  0.29
  26   17  0.71

ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50


Consensus pattern (25 bp):   
TTTTTTAAATTAAAATTACAAAAGG

Found at i:8152 original size:45 final size:45

Alignment explanation


    Indices: 8095--8269  Score: 166
    Period size: 45  Copynumber: 4.0  Consensus size: 45

       8085 ACCGCGGCCG

                  *                                      
       8095 CTGCCATTGCCACCTCCACTTTCAGTTCCAGAAGCACCCCAACCA
          1 CTGCCACTGCCACCTCCACTTTCAGTTCCAGAAGCACCCCAACCA

                   *          *  **    *    **    *   *   
       8140 CTGCCACCGCCA-CTGCCGC-CCCA--ACCA-CTGC-CACC-GCCA
          1 CTGCCACTGCCACCT-CCACTTTCAGTTCCAGAAGCACCCCAACCA

                  *     **                              *
       8179 CTGCCATTGCCATTTCCACTTTCAGTTCCAGAAGCACCCCAACCG
          1 CTGCCACTGCCACCTCCACTTTCAGTTCCAGAAGCACCCCAACCA

                                                         
       8224 CTGCCACTGCCACCTCCACTTTCAGTTCCAGAAGCACCCCAACCA
          1 CTGCCACTGCCACCTCCACTTTCAGTTCCAGAAGCACCCCAACCA

             
       8269 C
          1 C

       8270 CAGGGAAATC


Statistics
Matches: 96,  Mismatches: 26, Indels: 16
        0.70            0.19        0.12

Matches are distributed among these distances:
  39   16  0.17
  40    6  0.06
  41    2  0.02
  42    6  0.06
  43    2  0.02
  44    7  0.07
  45   57  0.59

ACGTcount: A:0.22, C:0.47, G:0.13, T:0.18


Consensus pattern (45 bp):   
CTGCCACTGCCACCTCCACTTTCAGTTCCAGAAGCACCCCAACCA

Found at i:8161 original size:27 final size:27

Alignment explanation


    Indices: 8131--8183  Score: 106
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       8121 TCCAGAAGCA

                                       
       8131 CCCCAACCACTGCCACCGCCACTGCCG
          1 CCCCAACCACTGCCACCGCCACTGCCG

                                      
       8158 CCCCAACCACTGCCACCGCCACTGCC
          1 CCCCAACCACTGCCACCGCCACTGCC

       8184 ATTGCCATTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.19, C:0.60, G:0.13, T:0.08


Consensus pattern (27 bp):   
CCCCAACCACTGCCACCGCCACTGCCG

Found at i:8190 original size:12 final size:12

Alignment explanation


    Indices: 8137--8184  Score: 51
    Period size: 12  Copynumber: 3.8  Consensus size: 12

       8127 AGCACCCCAA

                        
       8137 CCACTGCCACCG
          1 CCACTGCCACCG

                      *   *
       8149 CCACTGCCGCCCCAA
          1 CCACTG-C-CACC-G

                        
       8164 CCACTGCCACCG
          1 CCACTGCCACCG

                     
       8176 CCACTGCCA
          1 CCACTGCCA

       8185 TTGCCATTTC


Statistics
Matches: 29,  Mismatches: 4, Indels: 6
        0.74            0.10        0.15

Matches are distributed among these distances:
  12   15  0.52
  13    4  0.14
  14    4  0.14
  15    6  0.21

ACGTcount: A:0.19, C:0.58, G:0.15, T:0.08


Consensus pattern (12 bp):   
CCACTGCCACCG

Found at i:17990 original size:3 final size:3

Alignment explanation


    Indices: 17984--18023  Score: 64
    Period size: 3  Copynumber: 13.7  Consensus size: 3

      17974 TTTGTTGTTA

                                                         *        
      17984 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TGT TAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA

      18024 GTTGAATATT


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   2    2  0.06
   3   32  0.94

ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68


Consensus pattern (3 bp):   
TAT

Done.