Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006600.1 Kokia drynarioides strain JFW-HI SEQ_121189, 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: 6377
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29


Found at i:2420 original size:18 final size:17

Alignment explanation


    Indices: 2386--2420  Score: 52
    Period size: 18  Copynumber: 2.0  Consensus size: 17

       2376 AGAAAAGAGT

                        *    
       2386 GAAAATGAAAAAGAAAA
          1 GAAAATGAAAAAAAAAA

                              
       2403 GAAAATTGAAAAAAAAAA
          1 GAAAA-TGAAAAAAAAAA

       2421 TAAGGAAAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    5  0.31
  18   11  0.69

ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09


Consensus pattern (17 bp):   
GAAAATGAAAAAAAAAA

Found at i:2489 original size:25 final size:24

Alignment explanation


    Indices: 2427--2489  Score: 67
    Period size: 25  Copynumber: 2.7  Consensus size: 24

       2417 AAAATAAGGA

                    *          *    
       2427 AAAATG-AGAGAAA-AGAGCAAAG
          1 AAAATGAAAAGAAAGAGAGAAAAG

               *                    
       2449 AAAGTGAAAAGAAAGAGAGAAAAG
          1 AAAATGAAAAGAAAGAGAGAAAAG

                        *    
       2473 AAAAATGAAAAGGAAGA
          1 -AAAATGAAAAGAAAGA

       2490 AAAAGAGATA


Statistics
Matches: 33,  Mismatches: 5, Indels: 3
        0.80            0.12        0.07

Matches are distributed among these distances:
  22    5  0.15
  23    6  0.18
  24    8  0.24
  25   14  0.42

ACGTcount: A:0.67, C:0.02, G:0.27, T:0.05


Consensus pattern (24 bp):   
AAAATGAAAAGAAAGAGAGAAAAG

Found at i:2495 original size:31 final size:31

Alignment explanation


    Indices: 2425--2497  Score: 80
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       2415 AAAAAATAAG

                               *            
       2425 GAAAAATGAGAGAAAAGAGCAAAGAAAGTGAA
          1 GAAAAA-GAGAGAAAAGAGAAAAGAAAGTGAA

                                              
       2457 -AAGAAAGAGAGAAAAGA-AAAATGAAAAG-GAA
          1 GAA-AAAGAGAGAAAAGAGAAAA-G-AAAGTGAA

                      
       2488 GAAAAAGAGA
          1 GAAAAAGAGA

       2498 TAGAAAAATT


Statistics
Matches: 36,  Mismatches: 1, Indels: 9
        0.78            0.02        0.20

Matches are distributed among these distances:
  30    3  0.08
  31   24  0.67
  32    9  0.25

ACGTcount: A:0.67, C:0.01, G:0.27, T:0.04


Consensus pattern (31 bp):   
GAAAAAGAGAGAAAAGAGAAAAGAAAGTGAA
Done.