Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009284.1 Kokia drynarioides strain JFW-HI SEQ_123989, 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: 2257
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.40


Found at i:81 original size:13 final size:14

Alignment explanation


    Indices: 55--83  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

         45 CATATATTTC

                          
         55 ATTATTTATTAAAT
          1 ATTATTTATTAAAT

                          
         69 ATTATTT-TTAAAT
          1 ATTATTTATTAAAT

              
         82 AT
          1 AT

         84 AAATCAGTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    8  0.53
  14    7  0.47

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (14 bp):   
ATTATTTATTAAAT

Found at i:782 original size:24 final size:24

Alignment explanation


    Indices: 734--787  Score: 65
    Period size: 25  Copynumber: 2.2  Consensus size: 24

        724 AATTTTTTTT

                     **             
        734 ATAAAAAATTGAAAATCAAATTTA
          1 ATAAAAAATAAAAAATCAAATTTA

                             *       
        758 ATTAAAAAATAAAAAATTAAA-TTA
          1 A-TAAAAAATAAAAAATCAAATTTA

                  
        782 ATAAAA
          1 ATAAAA

        788 GATGCAAAAG


Statistics
Matches: 26,  Mismatches: 3, Indels: 3
        0.81            0.09        0.09

Matches are distributed among these distances:
  23    5  0.19
  24    5  0.19
  25   16  0.62

ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28


Consensus pattern (24 bp):   
ATAAAAAATAAAAAATCAAATTTA

Found at i:1137 original size:17 final size:17

Alignment explanation


    Indices: 1115--1158  Score: 70
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       1105 AAAAGTCTTA

                             
       1115 TTTAAAAATATTTTTAT
          1 TTTAAAAATATTTTTAT

                             
       1132 TTTAAAAATATTTTTAT
          1 TTTAAAAATATTTTTAT

            * *       
       1149 CTCAAAAATA
          1 TTTAAAAATA

       1159 CTCATTAAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  17   25  1.00

ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50


Consensus pattern (17 bp):   
TTTAAAAATATTTTTAT

Found at i:1770 original size:18 final size:19

Alignment explanation


    Indices: 1734--1770  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       1724 TCTTTATATC

                    *          
       1734 AATAAAAGTTATATGTAAT
          1 AATAAAAGATATATGTAAT

                               
       1753 AATAAAAGATAT-TGTAAT
          1 AATAAAAGATATATGTAAT

       1771 TAAAATATAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    6  0.35
  19   11  0.65

ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35


Consensus pattern (19 bp):   
AATAAAAGATATATGTAAT
Done.