Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005135.1 Kokia drynarioides strain JFW-HI SEQ_118972, 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, 696

Length: 1161
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34


Found at i:510 original size:16 final size:16

Alignment explanation


    Indices: 491--521  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        481 AATATGTTTG

                            
        491 AATTTATTTTAAATTT
          1 AATTTATTTTAAATTT

                           
        507 AATTTATTTTAAATT
          1 AATTTATTTTAAATT

        522 AAAATTAATT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (16 bp):   
AATTTATTTTAAATTT

Found at i:584 original size:14 final size:13

Alignment explanation


    Indices: 536--585  Score: 55
    Period size: 14  Copynumber: 3.6  Consensus size: 13

        526 TTAATTAAAA

                     *    
        536 AAAGTCCCACATAC
          1 AAAGT-CCAAATAC

                *         
        550 AAAGCCCAAATTAC
          1 AAAGTCCAAA-TAC

                         
        564 AAAGTCCAAATAC
          1 AAAGTCCAAATAC

                     
        577 AAATGTCCA
          1 AAA-GTCCA

        586 TTTTAACAGG


Statistics
Matches: 31,  Mismatches: 3, Indels: 4
        0.82            0.08        0.11

Matches are distributed among these distances:
  13   10  0.32
  14   21  0.68

ACGTcount: A:0.48, C:0.28, G:0.08, T:0.16


Consensus pattern (13 bp):   
AAAGTCCAAATAC

Found at i:751 original size:22 final size:25

Alignment explanation


    Indices: 710--760  Score: 81
    Period size: 22  Copynumber: 2.2  Consensus size: 25

        700 CGTCAGCATA

                                     
        710 ACCAGCAGCTCACCAGCCCCTCTGC
          1 ACCAGCAGCTCACCAGCCCCTCTGC

                                     
        735 ACCAGC-GC-CACCA-CCCCTCTGC
          1 ACCAGCAGCTCACCAGCCCCTCTGC

                
        757 ACCA
          1 ACCA

        761 ACACCACTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  22   13  0.50
  23    5  0.19
  24    2  0.08
  25    6  0.23

ACGTcount: A:0.22, C:0.55, G:0.14, T:0.10


Consensus pattern (25 bp):   
ACCAGCAGCTCACCAGCCCCTCTGC

Found at i:767 original size:22 final size:23

Alignment explanation


    Indices: 720--767  Score: 71
    Period size: 22  Copynumber: 2.1  Consensus size: 23

        710 ACCAGCAGCT

                               * * 
        720 CACCAGCCCCTCTGCACCAGCGC
          1 CACCAGCCCCTCTGCACCAACAC

                                   
        743 CACCA-CCCCTCTGCACCAACAC
          1 CACCAGCCCCTCTGCACCAACAC

               
        765 CAC
          1 CAC

        768 TGTAAACCTG


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

Matches are distributed among these distances:
  22   18  0.78
  23    5  0.22

ACGTcount: A:0.23, C:0.58, G:0.10, T:0.08


Consensus pattern (23 bp):   
CACCAGCCCCTCTGCACCAACAC

Found at i:1141 original size:3 final size:3

Alignment explanation


    Indices: 1133--1161  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

       1123 GTATTAAATG

                                                  
       1133 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (3 bp):   
AAT

Done.