Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012765.1 Kokia drynarioides strain JFW-HI SEQ_127777, 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: 9611
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34

Warning! 20 characters in sequence are not A, C, G, or T


Found at i:6381 original size:19 final size:20

Alignment explanation


    Indices: 6344--6395  Score: 56
    Period size: 19  Copynumber: 2.7  Consensus size: 20

       6334 TTTATTTTAT

                                
       6344 ATAATTTATATATTATAAAA
          1 ATAATTTATATATTATAAAA

                                *
       6364 ATAATTT-TAT-TGTATAAAT
          1 ATAATTTATATAT-TATAAAA

               *          
       6383 AT-TTTTATATATT
          1 ATAATTTATATATT

       6396 TTTTCAATTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 7
        0.75            0.06        0.19

Matches are distributed among these distances:
  18    4  0.15
  19   15  0.56
  20    8  0.30

ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54


Consensus pattern (20 bp):   
ATAATTTATATATTATAAAA

Found at i:6405 original size:9 final size:8

Alignment explanation


    Indices: 6383--6452  Score: 54
    Period size: 9  Copynumber: 8.2  Consensus size: 8

       6373 TTGTATAAAT

                     
       6383 ATTTTTATA
          1 ATTTTT-TA

                      
       6392 TATTTTTTCA
          1 -ATTTTTT-A

                    
       6402 ATTTTTTA
          1 ATTTTTTA

                    
       6410 ATTTTTTA
          1 ATTTTTTA

               *  *  
       6418 TATATTATA
          1 -ATTTTTTA

                      
       6427 TATATTTTTA
          1 -AT-TTTTTA

                    
       6437 A--TTTTA
          1 ATTTTTTA

                    
       6443 ATTTTTTA
          1 ATTTTTTA

              
       6451 AT
          1 AT

       6453 GGATGCCATG


Statistics
Matches: 51,  Mismatches: 4, Indels: 12
        0.76            0.06        0.18

Matches are distributed among these distances:
   6    6  0.12
   8   16  0.31
   9   18  0.35
  10   11  0.22

ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69


Consensus pattern (8 bp):   
ATTTTTTA

Found at i:6433 original size:28 final size:27

Alignment explanation


    Indices: 6384--6441  Score: 73
    Period size: 28  Copynumber: 2.1  Consensus size: 27

       6374 TGTATAAATA

                        * *             
       6384 TTTTTATATATTTTTTCAATTTTTTAAT
          1 TTTTTATATATTATATCAA-TTTTTAAT

                                        
       6412 TTTTTATATATTATAT-ATATTTTTAAT
          1 TTTTTATATATTATATCA-ATTTTTAAT

               
       6439 TTT
          1 TTT

       6442 AATTTTTTAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  27   12  0.44
  28   15  0.56

ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71


Consensus pattern (27 bp):   
TTTTTATATATTATATCAATTTTTAAT

Found at i:8157 original size:6 final size:6

Alignment explanation


    Indices: 8146--8171  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

       8136 TGATCAAAAT

                                          
       8146 TGAAAG TGAAAG TGAAAG TGAAAG TG
          1 TGAAAG TGAAAG TGAAAG TGAAAG TG

       8172 TAACACCCTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19


Consensus pattern (6 bp):   
TGAAAG

Found at i:8640 original size:23 final size:23

Alignment explanation


    Indices: 8588--8736  Score: 156
    Period size: 23  Copynumber: 6.3  Consensus size: 23

       8578 TATACGGAAC

                          *        
       8588 AAACAGAGAGCACATA-AGTGCT
          1 AAACAGAGAGCACACACAGTGCT

               *                      
       8610 GGGCAACAGAGAGCACACACAGTGCT
          1 ---AAACAGAGAGCACACACAGTGCT

                          * *   *  
       8636 AAACAGAGAGCACAAAAAGTACT
          1 AAACAGAGAGCACACACAGTGCT

              *             * *    
       8659 AATCAGAGAGCACACAAAATGCT
          1 AAACAGAGAGCACACACAGTGCT

              *                    
       8682 AATCAGAGAGCACACACAGTGCT
          1 AAACAGAGAGCACACACAGTGCT

                                     
       8705 AATAACAGAGAGCACACACAGTGCT
          1 -A-AACAGAGAGCACACACAGTGCT

              *    
       8730 AATCAGA
          1 AAACAGA

       8737 AGCGCGCTAG


Statistics
Matches: 107,  Mismatches: 14, Indels: 8
        0.83            0.11        0.06

Matches are distributed among these distances:
  23   64  0.60
  24    2  0.02
  25   35  0.33
  26    6  0.06

ACGTcount: A:0.45, C:0.22, G:0.21, T:0.11


Consensus pattern (23 bp):   
AAACAGAGAGCACACACAGTGCT

Found at i:8645 original size:25 final size:23

Alignment explanation


    Indices: 8616--8736  Score: 170
    Period size: 23  Copynumber: 5.2  Consensus size: 23

       8606 TGCTGGGCAA

                                  *
       8616 CAGAGAGCACACACAGTGCTAAA
          1 CAGAGAGCACACACAGTGCTAAT

                       * *   *     
       8639 CAGAGAGCACAAAAAGTACTAAT
          1 CAGAGAGCACACACAGTGCTAAT

                         * *       
       8662 CAGAGAGCACACAAAATGCTAAT
          1 CAGAGAGCACACACAGTGCTAAT

                                   
       8685 CAGAGAGCACACACAGTGCTAAT
          1 CAGAGAGCACACACAGTGCTAAT

                                     
       8708 AACAGAGAGCACACACAGTGCTAAT
          1 --CAGAGAGCACACACAGTGCTAAT

                
       8733 CAGA
          1 CAGA

       8737 AGCGCGCTAG


Statistics
Matches: 87,  Mismatches: 9, Indels: 4
        0.87            0.09        0.04

Matches are distributed among these distances:
  23   64  0.74
  25   23  0.26

ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12


Consensus pattern (23 bp):   
CAGAGAGCACACACAGTGCTAAT

Done.