Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002707.1 Kokia drynarioides strain JFW-HI SEQ_114993, 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: 23556
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:49 original size:2 final size:2

Alignment explanation


    Indices: 1--36  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

                                                                 
          1 TA TA 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 TA TA

         37 AATGGTTTAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:543 original size:24 final size:23

Alignment explanation


    Indices: 515--570  Score: 67
    Period size: 23  Copynumber: 2.4  Consensus size: 23

        505 TAGACTAATA

                   *               *
        515 AGAGTTTGACTCAAACAAATAAAT
          1 AGAGTTTAACTCAAA-AAATAAAC

                     * *           
        539 AGAGTTTAATTGAAAAAATAAAC
          1 AGAGTTTAACTCAAAAAATAAAC

                     
        562 AGAGTTTAA
          1 AGAGTTTAA

        571 TTGAAAGATT


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  23   16  0.57
  24   12  0.43

ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27


Consensus pattern (23 bp):   
AGAGTTTAACTCAAAAAATAAAC

Found at i:560 original size:23 final size:23

Alignment explanation


    Indices: 531--576  Score: 83
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        521 TGACTCAAAC

                   *               
        531 AAATAAATAGAGTTTAATTGAAA
          1 AAATAAACAGAGTTTAATTGAAA

                                   
        554 AAATAAACAGAGTTTAATTGAAA
          1 AAATAAACAGAGTTTAATTGAAA

        577 GATTATTTCT


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.57, C:0.02, G:0.13, T:0.28


Consensus pattern (23 bp):   
AAATAAACAGAGTTTAATTGAAA

Found at i:3288 original size:2 final size:2

Alignment explanation


    Indices: 3281--3309  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       3271 AAATCAAGTA

                                                       
       3281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       3310 CACAAAGCAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:16603 original size:21 final size:21

Alignment explanation


    Indices: 16577--16618  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      16567 ATGAAAACTT

                                 
      16577 CCTCCTTTGTAACCATTTGAC
          1 CCTCCTTTGTAACCATTTGAC

                                 
      16598 CCTCCTTTGTAACCATTTGAC
          1 CCTCCTTTGTAACCATTTGAC

      16619 TAATTAACAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.19, C:0.33, G:0.10, T:0.38


Consensus pattern (21 bp):   
CCTCCTTTGTAACCATTTGAC

Found at i:18707 original size:20 final size:20

Alignment explanation


    Indices: 18662--18700  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      18652 AATTAAGTTA

                      *         
      18662 GTTTAATTAATTTAATTATG
          1 GTTTAATTAACTTAATTATG

                               
      18682 GTTTAATTAACTTAATTAT
          1 GTTTAATTAACTTAATTAT

      18701 TTCTTAAACA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.36, C:0.03, G:0.08, T:0.54


Consensus pattern (20 bp):   
GTTTAATTAACTTAATTATG

Found at i:19080 original size:12 final size:12

Alignment explanation


    Indices: 19063--19102  Score: 53
    Period size: 12  Copynumber: 3.3  Consensus size: 12

      19053 GAACTTAATG

                        
      19063 CTACTGTTACTA
          1 CTACTGTTACTA

                  *     
      19075 CTACTGCTACTA
          1 CTACTGTTACTA

              *        *
      19087 CTTCTGTTACTG
          1 CTACTGTTACTA

                
      19099 CTAC
          1 CTAC

      19103 CACTGTTATC


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  12   23  1.00

ACGTcount: A:0.20, C:0.30, G:0.10, T:0.40


Consensus pattern (12 bp):   
CTACTGTTACTA
Done.