Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008435.1 Kokia drynarioides strain JFW-HI SEQ_123106, 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: 4317
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40


Found at i:1485 original size:18 final size:18

Alignment explanation


    Indices: 1462--1496  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1452 ACCAAAACTT

                               
       1462 TATTTTAAATTTT-TTATA
          1 TATTTT-AATTTTATTATA

                             
       1480 TATTTTAATTTTATTAT
          1 TATTTTAATTTTATTAT

       1497 GCACATTTTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    6  0.38
  18   10  0.62

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (18 bp):   
TATTTTAATTTTATTATA

Found at i:1995 original size:21 final size:21

Alignment explanation


    Indices: 1969--2008  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1959 ATTATTTATT

                                  
       1969 ATATGTTATTTTAAA-ACATAA
          1 ATATG-TATTTTAAATACATAA

                  *            
       1990 ATATGTGTTTTAAATACAT
          1 ATATGTATTTTAAATACAT

       2009 GCATGGTTTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

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

ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45


Consensus pattern (21 bp):   
ATATGTATTTTAAATACATAA

Found at i:2706 original size:16 final size:16

Alignment explanation


    Indices: 2685--2715  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       2675 TTTTTTTAAA

                    *       
       2685 AAATTCATCAAATTAT
          1 AAATTCATAAAATTAT

                           
       2701 AAATTCATAAAATTA
          1 AAATTCATAAAATTA

       2716 AATTTTAACT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35


Consensus pattern (16 bp):   
AAATTCATAAAATTAT

Found at i:3312 original size:21 final size:21

Alignment explanation


    Indices: 3288--3334  Score: 58
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       3278 AGGTTTAAAA

                        *        
       3288 TTTTAAAATTAGGGTTTAGGT
          1 TTTTAAAATTAGAGTTTAGGT

                *            *   
       3309 TTTTTAAATTAGAGTTTTGGT
          1 TTTTAAAATTAGAGTTTAGGT

            *    
       3330 ATTTA
          1 TTTTA

       3335 TTTTATATAT


Statistics
Matches: 21,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53


Consensus pattern (21 bp):   
TTTTAAAATTAGAGTTTAGGT
Done.