Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010657.1 Kokia drynarioides strain JFW-HI SEQ_125600, 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: 15355
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36


Found at i:2053 original size:21 final size:21

Alignment explanation


    Indices: 2029--2091  Score: 67
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       2019 CGACAATAAC

                                 
       2029 AATATCATATATTTAAAAGAT
          1 AATATCATATATTTAAAAGAT

                              * *  
       2050 AATA-CATTTATATTTAATATAT
          1 AATATCA--TATATTTAAAAGAT

                                 
       2072 ATATAT-ATATATTTAAAAGA
          1 A-ATATCATATATTTAAAAGA

       2092 AGAAAAAACA


Statistics
Matches: 34,  Mismatches: 4, Indels: 8
        0.74            0.09        0.17

Matches are distributed among these distances:
  20    2  0.06
  21   15  0.44
  22   13  0.38
  23    4  0.12

ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43


Consensus pattern (21 bp):   
AATATCATATATTTAAAAGAT

Found at i:10939 original size:30 final size:30

Alignment explanation


    Indices: 10903--10960  Score: 80
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      10893 AAAAAAAATA

                        *   *             
      10903 TGTTAAACGATTTAAATTGAATTATTCTTT
          1 TGTTAAACGATTAAAAATGAATTATTCTTT

                   *               *    
      10933 TGTTAAAGGATTAAAAATGAATTTTTCT
          1 TGTTAAACGATTAAAAATGAATTATTCT

      10961 GTCTAATTAT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  30   24  1.00

ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47


Consensus pattern (30 bp):   
TGTTAAACGATTAAAAATGAATTATTCTTT

Found at i:14443 original size:15 final size:16

Alignment explanation


    Indices: 14409--14448  Score: 55
    Period size: 16  Copynumber: 2.6  Consensus size: 16

      14399 TAATATTAAA

                   *        
      14409 TAAATAAAAAATTATT
          1 TAAATAATAAATTATT

                            
      14425 TAAATAATAAATT-TT
          1 TAAATAATAAATTATT

                *    
      14440 TAAAAAATA
          1 TAAATAATA

      14449 TATTGATACG


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   10  0.45
  16   12  0.55

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (16 bp):   
TAAATAATAAATTATT

Found at i:14908 original size:17 final size:17

Alignment explanation


    Indices: 14886--14919  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      14876 AAAAAAATTC

                    *        
      14886 ATTTAAATGTTATTTAA
          1 ATTTAAATATTATTTAA

                             
      14903 ATTTAAATATTATTTAA
          1 ATTTAAATATTATTTAA

      14920 TCATGTAAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53


Consensus pattern (17 bp):   
ATTTAAATATTATTTAA

Found at i:15245 original size:2 final size:2

Alignment explanation


    Indices: 15240--15269  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      15230 TATTAAAACC

                                                        
      15240 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      15270 TATGATGCTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Done.