Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008758.1 Kokia drynarioides strain JFW-HI SEQ_123441, 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, 987

Length: 1646
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.39


Found at i:89 original size:17 final size:17

Alignment explanation


    Indices: 64--98  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

         54 TTTACATATT

                *            
         64 TTAAGTTACTTACTTGG
          1 TTAAATTACTTACTTGG

                        *    
         81 TTAAATTACTTAGTTGG
          1 TTAAATTACTTACTTGG

             
         98 T
          1 T

         99 CGCCCATATT


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

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49


Consensus pattern (17 bp):   
TTAAATTACTTACTTGG

Found at i:1352 original size:21 final size:20

Alignment explanation


    Indices: 1310--1370  Score: 52
    Period size: 20  Copynumber: 2.9  Consensus size: 20

       1300 AAATTATTTA

                                 
       1310 AATTAAAAAATTAGAAAAATT
          1 AATT-AAAAATTAGAAAAATT

                    *   *        
       1331 AATTAAAATTTATAAAATATT
          1 AATTAAAAATTAGAAAA-ATT

                    *           
       1352 -ATTAATATATTAAGAAAAA
          1 AATTAA-AAATT-AGAAAAA

       1371 ATATGAAAAA


Statistics
Matches: 32,  Mismatches: 5, Indels: 6
        0.74            0.12        0.14

Matches are distributed among these distances:
  20   16  0.50
  21   11  0.34
  22    5  0.16

ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34


Consensus pattern (20 bp):   
AATTAAAAATTAGAAAAATT

Found at i:1527 original size:18 final size:19

Alignment explanation


    Indices: 1504--1547  Score: 56
    Period size: 18  Copynumber: 2.4  Consensus size: 19

       1494 AAAAATTATA

                               
       1504 TATAAAACTATA-AAATTT
          1 TATAAAACTATATAAATTT

                   *           
       1522 TAT-AAATTATATAAATTT
          1 TATAAAACTATATAAATTT

                    
       1540 TATTAAAA
          1 TA-TAAAA

       1548 TGGTTAAAAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  17    7  0.32
  18   11  0.50
  19    1  0.05
  20    3  0.14

ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43


Consensus pattern (19 bp):   
TATAAAACTATATAAATTT
Done.