Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001717.1 Kokia drynarioides strain JFW-HI SEQ_113414, 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: 5738
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36


Found at i:1067 original size:29 final size:29

Alignment explanation


    Indices: 1007--1067  Score: 70
    Period size: 29  Copynumber: 2.1  Consensus size: 29

        997 TTACAACTAG

                          *         *    
       1007 TAAGAAAATATTATTAATTATTATGATGT
          1 TAAGAAAATATTATAAATTATTATAATGT

                 *                      * 
       1036 TAAGAGAATATTATCAAATTATT-TAATTT
          1 TAAGAAAATATTAT-AAATTATTATAATGT

               
       1065 TAA
          1 TAA

       1068 ATAGTTAATT


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  29   20  0.74
  30    7  0.26

ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44


Consensus pattern (29 bp):   
TAAGAAAATATTATAAATTATTATAATGT

Found at i:1585 original size:36 final size:36

Alignment explanation


    Indices: 1519--1666  Score: 161
    Period size: 36  Copynumber: 4.1  Consensus size: 36

       1509 TGGAGGTAAG

                *   *            *   *          
       1519 AGACGAGGCCAAAGATCAACCGCGATGTGCACATGA
          1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA

                      *           *         *   
       1555 AGACAAGGTCGAAGATCAACCCTGACGTGCACGTGA
          1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA

                *    *                      **  
       1591 AGACGAGGTTAAAGATCAACCCCGACGTGCACGCGA
          1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA

                    *              *  *      *  
       1627 AGACAAGGCCAAAGATCAACCCCAACATGCACAAGA
          1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA

                
       1663 AGAC
          1 AGAC

       1667 GGGGCCGAAG


Statistics
Matches: 93,  Mismatches: 19, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  36   93  1.00

ACGTcount: A:0.38, C:0.27, G:0.25, T:0.10


Consensus pattern (36 bp):   
AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA

Found at i:1658 original size:72 final size:72

Alignment explanation


    Indices: 1519--1679  Score: 187
    Period size: 72  Copynumber: 2.2  Consensus size: 72

       1509 TGGAGGTAAG

                                 *   *       *          * *           **  *  
       1519 AGACGAGGCCAAAGATCAACCGCGATGTGCACATGAAGACAAGGTCGAAGATCAACCCTGACGTG
          1 AGACGAGGCCAAAGATCAACCCCGACGTGCACACGAAGACAAGGCCAAAGATCAACCCCAACATG

               **  
       1584 CACGTGA
         66 CACAAGA

                    **                      *                                
       1591 AGACGAGGTTAAAGATCAACCCCGACGTGCACGCGAAGACAAGGCCAAAGATCAACCCCAACATG
          1 AGACGAGGCCAAAGATCAACCCCGACGTGCACACGAAGACAAGGCCAAAGATCAACCCCAACATG

                   
       1656 CACAAGA
         66 CACAAGA

                 *    *      
       1663 AGACGGGGCCGAAGATC
          1 AGACGAGGCCAAAGATC

       1680 TAGTGGAGTT


Statistics
Matches: 72,  Mismatches: 17, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  72   72  1.00

ACGTcount: A:0.37, C:0.27, G:0.27, T:0.10


Consensus pattern (72 bp):   
AGACGAGGCCAAAGATCAACCCCGACGTGCACACGAAGACAAGGCCAAAGATCAACCCCAACATG
CACAAGA

Done.