Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002137.1 Kokia drynarioides strain JFW-HI SEQ_114081, 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: 15940
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:10303 original size:15 final size:15

Alignment explanation


    Indices: 10285--10319  Score: 54
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      10275 TTTATATATT

                            
      10285 TTAATATTAAA-AAAA
          1 TTAA-ATTAAATAAAA

                           
      10300 TTAAATTAAATAAAA
          1 TTAAATTAAATAAAA

                 
      10315 TTAAA
          1 TTAAA

      10320 ATTTTACAAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    6  0.32
  15   13  0.68

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (15 bp):   
TTAAATTAAATAAAA

Found at i:10371 original size:27 final size:27

Alignment explanation


    Indices: 10330--10393  Score: 85
    Period size: 27  Copynumber: 2.4  Consensus size: 27

      10320 ATTTTACAAG

                              *        
      10330 TGGTGCCTTTAGGGTAGGTGGCACCAA
          1 TGGTGCCTTTAGGGTAGGCGGCACCAA

                                     * *
      10357 TGGTGCCTATT-GGGTAGGCGGCACTAG
          1 TGGTGCCT-TTAGGGTAGGCGGCACCAA

                      
      10384 TGGTGCCTTT
          1 TGGTGCCTTT

      10394 GTCAAAACTA


Statistics
Matches: 33,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  26    2  0.06
  27   29  0.88
  28    2  0.06

ACGTcount: A:0.14, C:0.19, G:0.38, T:0.30


Consensus pattern (27 bp):   
TGGTGCCTTTAGGGTAGGCGGCACCAA

Found at i:13277 original size:28 final size:28

Alignment explanation


    Indices: 13224--13281  Score: 73
    Period size: 28  Copynumber: 2.1  Consensus size: 28

      13214 CATTTTTTTG

                                *       
      13224 TTGGAATTAATTAAGTTTATGATTGAAT
          1 TTGGAATTAATTAAGTTTATAATTGAAT

                        **               
      13252 TTGGAATTAATTCTGTTTA-AATTTGAAT
          1 TTGGAATTAATTAAGTTTATAA-TTGAAT

              
      13280 TT
          1 TT

      13282 ATTTAATAAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  27    1  0.04
  28   25  0.96

ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50


Consensus pattern (28 bp):   
TTGGAATTAATTAAGTTTATAATTGAAT

Found at i:13853 original size:6 final size:6

Alignment explanation


    Indices: 13842--13866  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

      13832 ATAGTGCTGT

                                         
      13842 GGCTCA GGCTCA GGCTCA GGCTCA G
          1 GGCTCA GGCTCA GGCTCA GGCTCA G

      13867 ACGGTTGAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16


Consensus pattern (6 bp):   
GGCTCA

Done.