Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008329.1 Kokia drynarioides strain JFW-HI SEQ_122995, 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: 3426
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36


Found at i:2693 original size:23 final size:23

Alignment explanation


    Indices: 2667--2757  Score: 79
    Period size: 21  Copynumber: 4.3  Consensus size: 23

       2657 TTGGTGTTTT

                      *            
       2667 TTTTTTTACTATTTTGGTTGCTG
          1 TTTTTTTACTGTTTTGGTTGCTG

                                   
       2690 --TTTTTACTGTTTTGG-TGC--
          1 TTTTTTTACTGTTTTGGTTGCTG

                          * *      
       2708 -TTTTTTACTGTTTCGATTGCTG
          1 TTTTTTTACTGTTTTGGTTGCTG

                    *      *    *  
       2730 TTTTTTTATTGTTTTAG-TGTTG
          1 TTTTTTTACTGTTTTGGTTGCTG

                  
       2752 TTTTTT
          1 TTTTTT

       2758 CTATTATTTT


Statistics
Matches: 55,  Mismatches: 8, Indels: 11
        0.74            0.11        0.15

Matches are distributed among these distances:
  19   13  0.24
  20    6  0.11
  21   14  0.25
  22   10  0.18
  23   12  0.22

ACGTcount: A:0.08, C:0.08, G:0.18, T:0.67


Consensus pattern (23 bp):   
TTTTTTTACTGTTTTGGTTGCTG

Found at i:2695 original size:21 final size:21

Alignment explanation


    Indices: 2669--2734  Score: 91
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       2659 GGTGTTTTTT

                    *            
       2669 TTTTTACTATTTTGGTTGCTG
          1 TTTTTACTGTTTTGGTTGCTG

                                 
       2690 TTTTTACTGTTTTGG-TGCT-
          1 TTTTTACTGTTTTGGTTGCTG

                        * *      
       2709 TTTTTACTGTTTCGATTGCTG
          1 TTTTTACTGTTTTGGTTGCTG

                 
       2730 TTTTT
          1 TTTTT

       2735 TTATTGTTTT


Statistics
Matches: 40,  Mismatches: 3, Indels: 4
        0.85            0.06        0.09

Matches are distributed among these distances:
  19   13  0.32
  20    8  0.20
  21   19  0.47

ACGTcount: A:0.08, C:0.11, G:0.18, T:0.64


Consensus pattern (21 bp):   
TTTTTACTGTTTTGGTTGCTG

Found at i:2797 original size:12 final size:12

Alignment explanation


    Indices: 2761--2798  Score: 58
    Period size: 12  Copynumber: 3.2  Consensus size: 12

       2751 GTTTTTTCTA

                        
       2761 TTATTTTTGTTG
          1 TTATTTTTGTTG

            *      *    
       2773 CTATTTTGGTTG
          1 TTATTTTTGTTG

                        
       2785 TTATTTTTGTTG
          1 TTATTTTTGTTG

              
       2797 TT
          1 TT

       2799 TGGATGTTTT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  12   22  1.00

ACGTcount: A:0.08, C:0.03, G:0.18, T:0.71


Consensus pattern (12 bp):   
TTATTTTTGTTG
Done.