Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007824.1 Kokia drynarioides strain JFW-HI SEQ_122460, 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: 7995
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36


Found at i:238 original size:16 final size:17

Alignment explanation


    Indices: 217--251  Score: 54
    Period size: 16  Copynumber: 2.1  Consensus size: 17

        207 TTTAAAAATT

                  *          
        217 ATAAAACATTCA-AAAA
          1 ATAAAAAATTCATAAAA

                             
        233 ATAAAAAATTCATAAAA
          1 ATAAAAAATTCATAAAA

              
        250 AT
          1 AT

        252 TTTAAAAAAT


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

Matches are distributed among these distances:
  16   11  0.65
  17    6  0.35

ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23


Consensus pattern (17 bp):   
ATAAAAAATTCATAAAA

Found at i:247 original size:27 final size:26

Alignment explanation


    Indices: 210--263  Score: 74
    Period size: 27  Copynumber: 2.0  Consensus size: 26

        200 TAATTAATTT

                                       
        210 AAAAATTATAAAACA-TTCAAAAAATA
          1 AAAAATTATAAAA-ATTTCAAAAAATA

                              *        
        236 AAAAATTCATAAAAATTTTAAAAAATA
          1 AAAAATT-ATAAAAATTTCAAAAAATA

             
        263 A
          1 A

        264 TCATAAAATA


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  26    8  0.32
  27   17  0.68

ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26


Consensus pattern (26 bp):   
AAAAATTATAAAAATTTCAAAAAATA

Found at i:377 original size:30 final size:31

Alignment explanation


    Indices: 331--393  Score: 85
    Period size: 30  Copynumber: 2.1  Consensus size: 31

        321 AAATTTTAAT

                                 *          
        331 AATCAATATATTTATAAATTTTAAAAAA-TTA
          1 AATCAATATATTTAT-AATTTCAAAAAAGTTA

                     *                     
        362 AATCAA-ATTTTTATAATTTCAAAAAAGTTA
          1 AATCAATATATTTATAATTTCAAAAAAGTTA

              
        392 AA
          1 AA

        394 GTACAATTTG


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  29   11  0.38
  30   12  0.41
  31    6  0.21

ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40


Consensus pattern (31 bp):   
AATCAATATATTTATAATTTCAAAAAAGTTA

Found at i:3919 original size:12 final size:12

Alignment explanation


    Indices: 3902--3928  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       3892 CATACTATTA

                        
       3902 ATTGTTATGAAT
          1 ATTGTTATGAAT

                        
       3914 ATTGTTATGAAT
          1 ATTGTTATGAAT

               
       3926 ATT
          1 ATT

       3929 ATTAAATGGA


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

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52


Consensus pattern (12 bp):   
ATTGTTATGAAT

Found at i:4124 original size:8 final size:8

Alignment explanation


    Indices: 4111--4136  Score: 52
    Period size: 8  Copynumber: 3.2  Consensus size: 8

       4101 TGCAATACAA

                    
       4111 ATTCTCAT
          1 ATTCTCAT

                    
       4119 ATTCTCAT
          1 ATTCTCAT

                    
       4127 ATTCTCAT
          1 ATTCTCAT

              
       4135 AT
          1 AT

       4137 CCATCATTTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   18  1.00

ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50


Consensus pattern (8 bp):   
ATTCTCAT

Found at i:5226 original size:21 final size:20

Alignment explanation


    Indices: 5188--5226  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       5178 TTATTTGGTC

                   *     *      
       5188 TTTATAATTTATTTTTATTT
          1 TTTATAAATTATTATTATTT

                               
       5208 TTTATAAATTACTTATTAT
          1 TTTATAAATTA-TTATTAT

       5227 AAATTTTTAC


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20   10  0.62
  21    6  0.38

ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67


Consensus pattern (20 bp):   
TTTATAAATTATTATTATTT
Done.