Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004147.1 Kokia drynarioides strain JFW-HI SEQ_117350, 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, 661

Length: 1102
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37


Found at i:639 original size:23 final size:25

Alignment explanation


    Indices: 613--663  Score: 70
    Period size: 23  Copynumber: 2.1  Consensus size: 25

        603 AAATATTAAA

                                     
        613 AAAATTAATAAATA-AAAATA-TAT
          1 AAAATTAATAAATATAAAATAGTAT

                   *                  
        636 AAAATTATTAAATATTAAAATAGTAT
          1 AAAATTAATAAATA-TAAAATAGTAT

              
        662 AA
          1 AA

        664 TATAAATATT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  23   13  0.54
  25    6  0.25
  26    5  0.21

ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33


Consensus pattern (25 bp):   
AAAATTAATAAATATAAAATAGTAT

Found at i:645 original size:26 final size:25

Alignment explanation


    Indices: 603--663  Score: 61
    Period size: 25  Copynumber: 2.4  Consensus size: 25

        593 ATTCTAATGT

                                      
        603 AAATAT-TAAAAAAATTAATAAATAA
          1 AAATATATAAAAAAATTAA-AAATAA

                        **      *  * 
        628 AAATATATAAAATTATTAAATATTA
          1 AAATATATAAAAAAATTAAAAATAA

                       
        653 AAATAGTATAA
          1 AAATA-TATAA

        664 TATAAATATT


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  25   15  0.50
  26   15  0.50

ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33


Consensus pattern (25 bp):   
AAATATATAAAAAAATTAAAAATAA

Found at i:687 original size:24 final size:22

Alignment explanation


    Indices: 597--691  Score: 65
    Period size: 23  Copynumber: 4.3  Consensus size: 22

        587 AATATTATTC

                *                 
        597 TAATGTAAATATTAAAAAAAT-
          1 TAATATAAATATTAAAAAAATA

                         *    *      
        618 TAATAAATAAA-AATATATAAAAT-
          1 TAAT--ATAAATATTA-AAAAAATA

                             * *  
        641 T-AT-TAAATATTAAAATAGTA
          1 TAATATAAATATTAAAAAAATA

                                    
        661 TAATATAAATATTTAAAAAAATAA
          1 TAATATAAATA-TTAAAAAAAT-A

                   
        685 TAATATA
          1 TAATATA

        692 GGTGAACTTA


Statistics
Matches: 56,  Mismatches: 9, Indels: 15
        0.70            0.11        0.19

Matches are distributed among these distances:
  19    8  0.14
  20    4  0.07
  21    6  0.11
  22   11  0.20
  23   19  0.34
  24    8  0.14

ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35


Consensus pattern (22 bp):   
TAATATAAATATTAAAAAAATA
Done.