Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009788.1 Kokia drynarioides strain JFW-HI SEQ_124509, 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: 4151
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35


Found at i:2573 original size:58 final size:58

Alignment explanation


    Indices: 2505--2614  Score: 168
    Period size: 58  Copynumber: 1.9  Consensus size: 58

       2495 GAAAATTGAT

                            *                                          
       2505 TTTGGATTTAGTTTATGAGAGT-TTTTTAGGAATGAAATTATATTTGAGTTTAAAAATA
          1 TTTGGATTTAGTTTATAAGAGTCTTTTTA-GAATGAAATTATATTTGAGTTTAAAAATA

                 *             *                          *     
       2563 TTTGGGTTTAGTTTATAAGTGTCTTTTTAGAATGAAATTATATTTGGGTTTA
          1 TTTGGATTTAGTTTATAAGAGTCTTTTTAGAATGAAATTATATTTGAGTTTA

       2615 GTTTATAAGT


Statistics
Matches: 47,  Mismatches: 4, Indels: 2
        0.89            0.08        0.04

Matches are distributed among these distances:
  58   41  0.87
  59    6  0.13

ACGTcount: A:0.30, C:0.01, G:0.20, T:0.49


Consensus pattern (58 bp):   
TTTGGATTTAGTTTATAAGAGTCTTTTTAGAATGAAATTATATTTGAGTTTAAAAATA

Found at i:2607 original size:42 final size:42

Alignment explanation


    Indices: 2560--2662  Score: 190
    Period size: 42  Copynumber: 2.5  Consensus size: 42

       2550 GAGTTTAAAA

                                                       
       2560 ATATTTGGGTTTAGTTTATAAGTGTCTTTTT-AGAATGAAATT
          1 ATATTTGGGTTTAGTTTATAAGTGT-TTTTTAAGAATGAAATT

                                                      
       2602 ATATTTGGGTTTAGTTTATAAGTGTTTTTTAAGAATGAAATT
          1 ATATTTGGGTTTAGTTTATAAGTGTTTTTTAAGAATGAAATT

                               
       2644 ATATTTGGGTTTAGTTTAT
          1 ATATTTGGGTTTAGTTTAT

       2663 GGATGGGTTT


Statistics
Matches: 60,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
  41    5  0.08
  42   55  0.92

ACGTcount: A:0.28, C:0.01, G:0.19, T:0.51


Consensus pattern (42 bp):   
ATATTTGGGTTTAGTTTATAAGTGTTTTTTAAGAATGAAATT

Found at i:2899 original size:23 final size:23

Alignment explanation


    Indices: 2855--2900  Score: 56
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       2845 GAAAAAAATT

                        **         
       2855 CAACTCGATTCGTTTAACTCGAA
          1 CAACTCGATTCGAATAACTCGAA

                 *           *     
       2878 CAACTTGATTCGAATAATTCGAA
          1 CAACTCGATTCGAATAACTCGAA

       2901 ATTCAAAATT


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30


Consensus pattern (23 bp):   
CAACTCGATTCGAATAACTCGAA
Done.