Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002576.1 Kokia drynarioides strain JFW-HI SEQ_114777, 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: 11460
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:3629 original size:36 final size:35

Alignment explanation


    Indices: 3583--3651  Score: 120
    Period size: 36  Copynumber: 1.9  Consensus size: 35

       3573 CCTAAATTCT

                                               
       3583 AAGAGATTGCTTACAAGTCAAGTTAAACAAAATCA
          1 AAGAGATTGCTTACAAGTCAAGTTAAACAAAATCA

                         *                    
       3618 AAGAGAATTGCTTGCAAGTCAAGTTAAACAAAAT
          1 AAGAG-ATTGCTTACAAGTCAAGTTAAACAAAAT

       3652 ATATTATCTT


Statistics
Matches: 32,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  35    5  0.16
  36   27  0.84

ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23


Consensus pattern (35 bp):   
AAGAGATTGCTTACAAGTCAAGTTAAACAAAATCA

Found at i:3703 original size:24 final size:24

Alignment explanation


    Indices: 3670--3726  Score: 78
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       3660 TTTCTATAAG

                 *          *       
       3670 ATTTAGTAGCATAATATATTTAAC
          1 ATTTATTAGCATAATAAATTTAAC

                                 *  
       3694 ATTTATTAGCATAATAAATTTTAC
          1 ATTTATTAGCATAATAAATTTAAC

               *     
       3718 ATTAATTAG
          1 ATTTATTAG

       3727 AATTAGGCTT


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44


Consensus pattern (24 bp):   
ATTTATTAGCATAATAAATTTAAC

Found at i:6539 original size:2 final size:2

Alignment explanation


    Indices: 6532--6560  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       6522 GTCAACATGC

                                                       
       6532 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

       6561 ATGATCTCGA


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:6942 original size:18 final size:18

Alignment explanation


    Indices: 6903--6945  Score: 61
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       6893 GAATAGATTT

                             *
       6903 TTAATTAAATAATTTTAT
          1 TTAATTAAATAATTTTAA

                               
       6921 TTAATTAAA-AATTTTAAA
          1 TTAATTAAATAATTTT-AA

                   
       6939 TTAATTA
          1 TTAATTA

       6946 CACATTGAAC


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  17    6  0.26
  18   17  0.74

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (18 bp):   
TTAATTAAATAATTTTAA

Found at i:8648 original size:27 final size:27

Alignment explanation


    Indices: 8593--8648  Score: 62
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       8583 GACGAATCCT

                                *  *   
       8593 ATTTTTGTAATCGAATTCAATTTGAAA
          1 ATTTTTGTAATCGAATTCAAATTAAAA

                                         
       8620 ATTTTTCG-AATCGAA-TCAAATTAACAA
          1 ATTTTT-GTAATCGAATTCAAATTAA-AA

              
       8647 AT
          1 AT

       8649 CCTATTATTG


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  26    7  0.28
  27   17  0.68
  28    1  0.04

ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39


Consensus pattern (27 bp):   
ATTTTTGTAATCGAATTCAAATTAAAA

Found at i:9011 original size:21 final size:19

Alignment explanation


    Indices: 8982--9020  Score: 51
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       8972 AAATAACTCG

                                 
       8982 AATTATTTATTTCAAATTTTC
          1 AATTATTTA--TCAAATTTTC

                *             
       9003 AATTTTTTATCAAATTTT
          1 AATTATTTATCAAATTTT

       9021 TCGAATCGAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    9  0.53
  21    8  0.47

ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59


Consensus pattern (19 bp):   
AATTATTTATCAAATTTTC

Found at i:10582 original size:32 final size:32

Alignment explanation


    Indices: 10546--10611  Score: 132
    Period size: 32  Copynumber: 2.1  Consensus size: 32

      10536 ACGAGCAGGA

                                            
      10546 TTTTCCTTAGGACAAGGGCTAATTTGATTTGT
          1 TTTTCCTTAGGACAAGGGCTAATTTGATTTGT

                                            
      10578 TTTTCCTTAGGACAAGGGCTAATTTGATTTGT
          1 TTTTCCTTAGGACAAGGGCTAATTTGATTTGT

              
      10610 TT
          1 TT

      10612 CGTATAAGGC


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

Matches are distributed among these distances:
  32   34  1.00

ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45


Consensus pattern (32 bp):   
TTTTCCTTAGGACAAGGGCTAATTTGATTTGT
Done.