Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013292.1 Kokia drynarioides strain JFW-HI SEQ_128314, 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: 22754
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30


Found at i:7425 original size:20 final size:21

Alignment explanation


    Indices: 7389--7427  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       7379 GCATTTTTTA

                      *          
       7389 TTTACTTTTATTTGTTTCACT
          1 TTTACTTTTAGTTGTTTCACT

                               
       7410 TTTACTTTT-GTTGTTTCA
          1 TTTACTTTTAGTTGTTTCA

       7428 AATTCCTTGC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    8  0.47
  21    9  0.53

ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67


Consensus pattern (21 bp):   
TTTACTTTTAGTTGTTTCACT

Found at i:9588 original size:24 final size:24

Alignment explanation


    Indices: 9555--9605  Score: 68
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       9545 TTGTACGACA

                 *                   
       9555 GATAAGAAGAA-AAGAAGGCACAAG
          1 GATAAAAAGAAGAAGAA-GCACAAG

                                 *  
       9579 GATAAAAAGAAGAAGAAGCACTAG
          1 GATAAAAAGAAGAAGAAGCACAAG

               
       9603 GAT
          1 GAT

       9606 GAGGGTAAGC


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  24   19  0.79
  25    5  0.21

ACGTcount: A:0.57, C:0.08, G:0.27, T:0.08


Consensus pattern (24 bp):   
GATAAAAAGAAGAAGAAGCACAAG

Found at i:9750 original size:17 final size:18

Alignment explanation


    Indices: 9712--9750  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       9702 CTCATTTTTA

                         *    
       9712 TTGTCATTGCATTTTATT
          1 TTGTCATTGCATTCTATT

                           *  
       9730 TTGTCATTGCA-TCTCTT
          1 TTGTCATTGCATTCTATT

                
       9747 TTGT
          1 TTGT

       9751 TAACTTAGTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  17    8  0.42
  18   11  0.58

ACGTcount: A:0.13, C:0.15, G:0.13, T:0.59


Consensus pattern (18 bp):   
TTGTCATTGCATTCTATT

Found at i:13234 original size:77 final size:77

Alignment explanation


    Indices: 13141--13296  Score: 249
    Period size: 77  Copynumber: 2.0  Consensus size: 77

      13131 GAATAACCTT

                  *                               ***                        
      13141 GGAGTTTTTGAGTTAGATGCTATCTCTGCTTTGTCAACTTTCGTATCCTCATTGGCCAATATCAT
          1 GGAGTTCTTGAGTTAGATGCTATCTCTGCTTTGTCAACGCACGTATCCTCATTGGCCAATATCAT

                        
      13206 AAAGAATATGAA
         66 AAAGAATATGAA

                                                     *                     * 
      13218 GGAGTTCTTGAGTTAGATGCTATCTCTGCTTTGTCAACGCAGGTATCCTCATTGGCCAATATCGT
          1 GGAGTTCTTGAGTTAGATGCTATCTCTGCTTTGTCAACGCACGTATCCTCATTGGCCAATATCAT

                   *    
      13283 AAAGAATGTGAA
         66 AAAGAATATGAA

              
      13295 GG
          1 GG

      13297 GAACAGACGA


Statistics
Matches: 72,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  77   72  1.00

ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35


Consensus pattern (77 bp):   
GGAGTTCTTGAGTTAGATGCTATCTCTGCTTTGTCAACGCACGTATCCTCATTGGCCAATATCAT
AAAGAATATGAA
Done.