Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013523.1 Kokia drynarioides strain JFW-HI SEQ_128549, 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: 19702
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:810 original size:31 final size:31

Alignment explanation


    Indices: 753--811  Score: 75
    Period size: 31  Copynumber: 1.9  Consensus size: 31

        743 TACTTTAATT

                                 *         
        753 TGATCAATTTTAATTTCTATACTTTTTTAAC
          1 TGATCAATTTTAATTTCTATAATTTTTTAAC

                  *            *         
        784 TGATCACTTTTAA-TTCTTTTAATTTTTT
          1 TGATCAATTTTAATTTC-TATAATTTTTT

        812 TTTTAAATTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  30    3  0.12
  31   21  0.88

ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59


Consensus pattern (31 bp):   
TGATCAATTTTAATTTCTATAATTTTTTAAC

Found at i:12716 original size:2 final size:2

Alignment explanation


    Indices: 12711--12737  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      12701 AACTTTTTTA

                                                    
      12711 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

      12738 AAATCGGATC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:16369 original size:30 final size:31

Alignment explanation


    Indices: 16301--16372  Score: 83
    Period size: 30  Copynumber: 2.4  Consensus size: 31

      16291 ACAACAAGAG

                *         *            *   
      16301 GACTATTTTGTCACTTTTCGATAACTTTAGT
          1 GACTGTTTTGTCACATTTCGATAACTTGAGT

              *                *    *      
      16332 GATTGTTTTGTCACATTTCTA-AAGTTGAGT
          1 GACTGTTTTGTCACATTTCGATAACTTGAGT

                       
      16362 GACTGTTTTGT
          1 GACTGTTTTGT

      16373 TAAACGTAAT


Statistics
Matches: 34,  Mismatches: 7, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  30   17  0.50
  31   17  0.50

ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49


Consensus pattern (31 bp):   
GACTGTTTTGTCACATTTCGATAACTTGAGT

Found at i:16520 original size:30 final size:31

Alignment explanation


    Indices: 16466--16528  Score: 119
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      16456 GAAAAATGAT

                                           
      16466 TGTTTTGTCACATTTTCAAAAGTTGAGGGAC
          1 TGTTTTGTCACATTTTCAAAAGTTGAGGGAC

                                           
      16497 TGTTTTGTCACATTTTC-AAAGTTGAGGGAC
          1 TGTTTTGTCACATTTTCAAAAGTTGAGGGAC

              
      16527 TG
          1 TG

      16529 AAATGTAAAC


Statistics
Matches: 32,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  30   15  0.47
  31   17  0.53

ACGTcount: A:0.24, C:0.13, G:0.24, T:0.40


Consensus pattern (31 bp):   
TGTTTTGTCACATTTTCAAAAGTTGAGGGAC
Done.