Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013989.1 Kokia drynarioides strain JFW-HI SEQ_129020, 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: 17927
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:3411 original size:9 final size:9

Alignment explanation


    Indices: 3393--3429  Score: 51
    Period size: 9  Copynumber: 4.2  Consensus size: 9

       3383 TCACTTAAAA

                     
       3393 AAAAAG-AG
          1 AAAAAGAAG

                     
       3401 AAAAAGAAG
          1 AAAAAGAAG

                      
       3410 AAAGAA-AAG
          1 AAA-AAGAAG

                     
       3419 AAAAAGAAG
          1 AAAAAGAAG

              
       3428 AA
          1 AA

       3430 TAAATTGCTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 5
        0.84            0.00        0.16

Matches are distributed among these distances:
   8    8  0.31
   9   16  0.62
  10    2  0.08

ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00


Consensus pattern (9 bp):   
AAAAAGAAG

Found at i:10098 original size:18 final size:19

Alignment explanation


    Indices: 10071--10122  Score: 74
    Period size: 18  Copynumber: 2.9  Consensus size: 19

      10061 GAAACTCTAT

                               
      10071 ATCC-TTCTGGGATTTTAA
          1 ATCCTTTCTGGGATTTTAA

                               
      10089 AT-CTTTCTGGGATTTTAA
          1 ATCCTTTCTGGGATTTTAA

                    *        
      10107 ATCCTTT-AGGGATTTT
          1 ATCCTTTCTGGGATTTT

      10123 CATATAAATT


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  17    1  0.03
  18   26  0.84
  19    4  0.13

ACGTcount: A:0.21, C:0.13, G:0.17, T:0.48


Consensus pattern (19 bp):   
ATCCTTTCTGGGATTTTAA

Found at i:12104 original size:14 final size:16

Alignment explanation


    Indices: 12077--12108  Score: 50
    Period size: 14  Copynumber: 2.1  Consensus size: 16

      12067 TTAACTTAAT

                            
      12077 AAAAAATATAATTTGC
          1 AAAAAATATAATTTGC

                            
      12093 AAAAAAT-T-ATTTGC
          1 AAAAAATATAATTTGC

              
      12107 AA
          1 AA

      12109 TATTCACTTC


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

Matches are distributed among these distances:
  14    8  0.50
  15    1  0.06
  16    7  0.44

ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31


Consensus pattern (16 bp):   
AAAAAATATAATTTGC

Found at i:13131 original size:2 final size:2

Alignment explanation


    Indices: 13124--13155  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      13114 TTACAAAACT

                                                           
      13124 TA TA 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 TA TA

      13156 AATTGAAATT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
TA

Done.