Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006467.1 Kokia drynarioides strain JFW-HI SEQ_121050, 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: 24585
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:3295 original size:21 final size:21

Alignment explanation


    Indices: 3244--3296  Score: 61
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       3234 AAAGATAAAT

                                   
       3244 TAAATATTTCAATACATGTGGCA
          1 TAAA-ATTT-AATACATGTGGCA

               *               **
       3267 TAATATTTAATACATGTGGGG
          1 TAAAATTTAATACATGTGGCA

                     
       3288 TAAAATTTA
          1 TAAAATTTA

       3297 TTAGTATTAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  21   19  0.73
  22    4  0.15
  23    3  0.12

ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38


Consensus pattern (21 bp):   
TAAAATTTAATACATGTGGCA

Found at i:5952 original size:2 final size:2

Alignment explanation


    Indices: 5945--5991  Score: 76
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       5935 TTGATAAAAC

                                                             *  *         
       5945 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                   
       5987 TA TA T
          1 TA TA T

       5992 GTGTGTGTGT


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:16923 original size:27 final size:26

Alignment explanation


    Indices: 16862--16915  Score: 72
    Period size: 28  Copynumber: 2.0  Consensus size: 26

      16852 TTCTTAGATG

                *                     
      16862 AATACTTTTTTAGTCATTTTGACTCT
          1 AATATTTTTTTAGTCATTTTGACTCT

                        *               
      16888 AATTATTTTTTTGGATCATTTTGACTCT
          1 AA-TATTTTTTTAG-TCATTTTGACTCT

      16916 CAACTTTTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  26    2  0.08
  27    9  0.38
  28   13  0.54

ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56


Consensus pattern (26 bp):   
AATATTTTTTTAGTCATTTTGACTCT

Found at i:18120 original size:1 final size:1

Alignment explanation


    Indices: 18116--18140  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

      18106 NNNNNNNNNN

                                     
      18116 AAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAA

      18141 TGTTCCAAGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.