Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013770.1 Kokia drynarioides strain JFW-HI SEQ_128798, 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: 5623
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34


Found at i:2054 original size:21 final size:21

Alignment explanation


    Indices: 2028--2073  Score: 58
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       2018 ACCTGCTGTT

                    *           * 
       2028 GAGGAGGATG-TTGATGTTGGA
          1 GAGGAGGAAGTTTG-TGTTGAA

                                 
       2049 GAGGAGGAAGTTTGTGTTGAA
          1 GAGGAGGAAGTTTGTGTTGAA

                
       2070 GAGG
          1 GAGG

       2074 TAAAAGAGAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21   19  0.86
  22    3  0.14

ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26


Consensus pattern (21 bp):   
GAGGAGGAAGTTTGTGTTGAA

Found at i:2503 original size:17 final size:17

Alignment explanation


    Indices: 2481--2530  Score: 82
    Period size: 17  Copynumber: 2.9  Consensus size: 17

       2471 TGTTAGTAAG

                   *         
       2481 CATTGTCGTTACATTTT
          1 CATTGTCATTACATTTT

                             
       2498 CATTGTCATTACATTTT
          1 CATTGTCATTACATTTT

                      *     
       2515 CATTGTCATTGCATTT
          1 CATTGTCATTACATTT

       2531 AAATGTTAGT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   31  1.00

ACGTcount: A:0.20, C:0.18, G:0.10, T:0.52


Consensus pattern (17 bp):   
CATTGTCATTACATTTT

Found at i:2861 original size:2 final size:2

Alignment explanation


    Indices: 2854--2881  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       2844 TACAGCTACC

                                                     
       2854 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2882 GCTATAAATA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:5602 original size:18 final size:18

Alignment explanation


    Indices: 5579--5621  Score: 68
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       5569 TGTGGGCAAA

                              
       5579 ATAATTTGTAGAATCTAT
          1 ATAATTTGTAGAATCTAT

                      *   *   
       5597 ATAATTTGTATAATGTAT
          1 ATAATTTGTAGAATCTAT

                   
       5615 ATAATTT
          1 ATAATTT

       5622 TA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  18   23  1.00

ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49


Consensus pattern (18 bp):   
ATAATTTGTAGAATCTAT
Done.