Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001389.1 Kokia drynarioides strain JFW-HI SEQ_112871, 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: 73010
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:26609 original size:17 final size:17

Alignment explanation


    Indices: 26577--26610  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      26567 AAAGAGTACT

                     * *     
      26577 ATGAAATAATATATCTA
          1 ATGAAATAACACATCTA

                             
      26594 ATGAAATAACACATCTA
          1 ATGAAATAACACATCTA

      26611 GTATTAATAG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29


Consensus pattern (17 bp):   
ATGAAATAACACATCTA

Found at i:34598 original size:15 final size:15

Alignment explanation


    Indices: 34578--34607  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      34568 GCAATGACTT

                           
      34578 AAACAAACTTATCGC
          1 AAACAAACTTATCGC

                      *    
      34593 AAACAAACTTTTCGC
          1 AAACAAACTTATCGC

      34608 CCCCCACTGT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.43, C:0.27, G:0.07, T:0.23


Consensus pattern (15 bp):   
AAACAAACTTATCGC

Found at i:42987 original size:12 final size:12

Alignment explanation


    Indices: 42970--42994  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      42960 AAATACACTC

                        
      42970 TTTTTCTTTTTT
          1 TTTTTCTTTTTT

                        
      42982 TTTTTCTTTTTT
          1 TTTTTCTTTTTT

             
      42994 T
          1 T

      42995 CGTGTTATTC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92


Consensus pattern (12 bp):   
TTTTTCTTTTTT

Found at i:52854 original size:16 final size:16

Alignment explanation


    Indices: 52833--52864  Score: 55
    Period size: 17  Copynumber: 1.9  Consensus size: 16

      52823 TTTAACTTTT

                             
      52833 AAAAAATTGCAAAAAAA
          1 AAAAAATT-CAAAAAAA

                           
      52850 AAAAAATTCAAAAAA
          1 AAAAAATTCAAAAAA

      52865 TATATATTCA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    7  0.47
  17    8  0.53

ACGTcount: A:0.78, C:0.06, G:0.03, T:0.12


Consensus pattern (16 bp):   
AAAAAATTCAAAAAAA

Found at i:59724 original size:13 final size:13

Alignment explanation


    Indices: 59691--59725  Score: 52
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      59681 AGTAGTGACG

                    *    
      59691 TTTTTTTTCTTTT
          1 TTTTTTTTGTTTT

             *           
      59704 TCTTTTTTGTTTT
          1 TTTTTTTTGTTTT

                     
      59717 TTTTTTTTG
          1 TTTTTTTTG

      59726 GGGTTATATT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89


Consensus pattern (13 bp):   
TTTTTTTTGTTTT

Found at i:68933 original size:17 final size:18

Alignment explanation


    Indices: 68911--68955  Score: 58
    Period size: 17  Copynumber: 2.6  Consensus size: 18

      68901 TTAAAAATAG

                              
      68911 AGTTTTTTATTTTT-AAA
          1 AGTTTTTTATTTTTCAAA

                   *        * 
      68928 AGTTTTTAATTTTTCACA
          1 AGTTTTTTATTTTTCAAA

                       
      68946 A-TTTTTTATT
          1 AGTTTTTTATT

      68956 GAAAATATGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  17   21  0.88
  18    3  0.12

ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64


Consensus pattern (18 bp):   
AGTTTTTTATTTTTCAAA

Done.