Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008858.1 Kokia drynarioides strain JFW-HI SEQ_123544, 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: 14498
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30


Found at i:7297 original size:2 final size:2

Alignment explanation


    Indices: 7284--7326  Score: 68
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       7274 CTCAGAGCAC

                      *              *                                    
       7284 AG AG AG AA AG AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

             
       7326 A
          1 A

       7327 AATGCCTTTC


Statistics
Matches: 37,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.53, C:0.02, G:0.44, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:9674 original size:21 final size:21

Alignment explanation


    Indices: 9650--9701  Score: 58
    Period size: 18  Copynumber: 2.6  Consensus size: 21

       9640 CACATTTGGA

                         *       
       9650 AAATTTTTATAATTTTTTTTT
          1 AAATTTTTATAATGTTTTTTT

                                 
       9671 AAA--TTTAT-ATGTTTTTTT
          1 AAATTTTTATAATGTTTTTTT

                          
       9689 AAATTCTTT-TAAT
          1 AAATT-TTTATAAT

       9702 AAATAAAAAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 8
        0.74            0.03        0.23

Matches are distributed among these distances:
  18   12  0.46
  19    5  0.19
  20    1  0.04
  21    8  0.31

ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65


Consensus pattern (21 bp):   
AAATTTTTATAATGTTTTTTT

Found at i:11159 original size:56 final size:56

Alignment explanation


    Indices: 11097--11208  Score: 215
    Period size: 56  Copynumber: 2.0  Consensus size: 56

      11087 TTGGCTAAAG

                                                    *               
      11097 TAAAAATTCTGAAATTTTTATGGTAAAAAGATATTTGAGTTTAATTTCATAAACAT
          1 TAAAAATTCTGAAATTTTTATGGTAAAAAGATATTTGAGTCTAATTTCATAAACAT

                                                                    
      11153 TAAAAATTCTGAAATTTTTATGGTAAAAAGATATTTGAGTCTAATTTCATAAACAT
          1 TAAAAATTCTGAAATTTTTATGGTAAAAAGATATTTGAGTCTAATTTCATAAACAT

      11209 CAAGCGGAAT


Statistics
Matches: 55,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  56   55  1.00

ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40


Consensus pattern (56 bp):   
TAAAAATTCTGAAATTTTTATGGTAAAAAGATATTTGAGTCTAATTTCATAAACAT

Found at i:11607 original size:22 final size:22

Alignment explanation


    Indices: 11582--11630  Score: 89
    Period size: 22  Copynumber: 2.2  Consensus size: 22

      11572 GCACGCTTAT

                                  
      11582 TGTTTAGCACTGTGTGTGCTTC
          1 TGTTTAGCACTGTGTGTGCTTC

                *                 
      11604 TGTTCAGCACTGTGTGTGCTTC
          1 TGTTTAGCACTGTGTGTGCTTC

                 
      11626 TGTTT
          1 TGTTT

      11631 CCCTAGCACT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  22   25  1.00

ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47


Consensus pattern (22 bp):   
TGTTTAGCACTGTGTGTGCTTC

Done.