Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013481.1 Kokia drynarioides strain JFW-HI SEQ_128507, 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, 823

Length: 1373
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36


Found at i:307 original size:14 final size:14

Alignment explanation


    Indices: 288--315  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

        278 ATAGCTCACT

                          
        288 TAGCTTATTTATCC
          1 TAGCTTATTTATCC

                          
        302 TAGCTTATTTATCC
          1 TAGCTTATTTATCC

        316 ACTTGGCCCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50


Consensus pattern (14 bp):   
TAGCTTATTTATCC

Found at i:442 original size:23 final size:23

Alignment explanation


    Indices: 363--551  Score: 144
    Period size: 23  Copynumber: 8.5  Consensus size: 23

        353 TAAACGGAAC

                      *    *    *  
        363 AAACAGAGAGTAC-CGAAGTACT
          1 AAACAGAGAGCACACAAAGTGCT

                           *       
        385 AAACAGAGAGCACA-TAAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

               *    *             *   
        407 GGGCAACAAAGAGCACACAAAGCGCT
          1 ---AAACAGAGAGCACACAAAGTGCT

                      *   *        
        433 AAACAGAGAGTACATAAA--G-T
          1 AAACAGAGAGCACACAAAGTGCT

                  *                
        453 --AC--TGAGCACACAAAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

              *             *      
        472 AATCAGAGAGCACACACAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

              *            *       
        495 AATCAGAGAGCACACGAAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

                            *      
        518 AAACAGAGAGCACACACAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

              *        
        541 AATCAGAGAGC
          1 AAACAGAGAGC

        552 GCGCTAGTGT


Statistics
Matches: 132,  Mismatches: 23, Indels: 23
        0.74            0.13        0.13

Matches are distributed among these distances:
  16    9  0.07
  18    3  0.02
  19    1  0.01
  20    1  0.01
  21    2  0.02
  22   18  0.14
  23   80  0.61
  25   12  0.09
  26    6  0.05

ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12


Consensus pattern (23 bp):   
AAACAGAGAGCACACAAAGTGCT

Found at i:508 original size:46 final size:46

Alignment explanation


    Indices: 456--551  Score: 174
    Period size: 46  Copynumber: 2.1  Consensus size: 46

        446 ATAAAGTACT

                              *                           
        456 GAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGA
          1 GAGCACACAAAGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA

                    *                                     
        502 GAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA
          1 GAGCACACAAAGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA

                
        548 GAGC
          1 GAGC

        552 GCGCTAGTGT


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  46   48  1.00

ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11


Consensus pattern (46 bp):   
GAGCACACAAAGTGCTAAACAGAGAGCACACACAGTGCTAATCAGA
Done.