Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007897.1 Kokia drynarioides strain JFW-HI SEQ_122538, 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: 7591
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36


Found at i:5236 original size:7 final size:7

Alignment explanation


    Indices: 5224--5269  Score: 56
    Period size: 7  Copynumber: 6.6  Consensus size: 7

       5214 AAAACATCAA

                   
       5224 AAATTTG
          1 AAATTTG

                  *
       5231 AAATTTA
          1 AAATTTG

                 **
       5238 AAATTCA
          1 AAATTTG

                   
       5245 AAATTTG
          1 AAATTTG

                   
       5252 AAATTTG
          1 AAATTTG

                 * 
       5259 AAATTCG
          1 AAATTTG

                
       5266 AAAT
          1 AAAT

       5270 CCAAAATCTA


Statistics
Matches: 34,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
   7   34  1.00

ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37


Consensus pattern (7 bp):   
AAATTTG

Found at i:5249 original size:21 final size:21

Alignment explanation


    Indices: 5223--5269  Score: 76
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       5213 TAAAACATCA

                                 
       5223 AAAATTTGAAATTTAAAATTC
          1 AAAATTTGAAATTTAAAATTC

                          *      
       5244 AAAATTTGAAATTTGAAATTC
          1 AAAATTTGAAATTTAAAATTC

            *    
       5265 GAAAT
          1 AAAAT

       5270 CCAAAATCTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36


Consensus pattern (21 bp):   
AAAATTTGAAATTTAAAATTC

Found at i:6089 original size:15 final size:15

Alignment explanation


    Indices: 6033--6090  Score: 53
    Period size: 15  Copynumber: 3.6  Consensus size: 15

       6023 TTTTATACTA

                           
       6033 TAAAATATTTATTAT
          1 TAAAATATTTATTAT

            *  *        *   
       6048 GAATATATTTATAATT
          1 TAAAATATTTATTA-T

                              
       6064 GTAATAAATATTTATTAT
          1 -T-A-AAATATTTATTAT

                     
       6082 TAAAATATT
          1 TAAAATATT

       6091 AATATTGAAT


Statistics
Matches: 33,  Mismatches: 6, Indels: 8
        0.70            0.13        0.17

Matches are distributed among these distances:
  15   18  0.55
  16    2  0.06
  17    1  0.03
  18    2  0.06
  19   10  0.30

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (15 bp):   
TAAAATATTTATTAT

Found at i:6198 original size:16 final size:19

Alignment explanation


    Indices: 6179--6228  Score: 52
    Period size: 18  Copynumber: 2.6  Consensus size: 19

       6169 TGAAATATTA

                               
       6179 AATAATTTATTAA-A-A-T
          1 AATAATTTATTAATATACT

                                  
       6195 AATAAATTATATTAATTATACT
          1 AAT-AATT-TATTAA-TATACT

                        
       6217 AATAATTTATTA
          1 AATAATTTATTA

       6229 TATGATTAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
  16    3  0.11
  17    4  0.14
  18    6  0.21
  20    6  0.21
  21    5  0.18
  22    4  0.14

ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46


Consensus pattern (19 bp):   
AATAATTTATTAATATACT

Found at i:6265 original size:14 final size:14

Alignment explanation


    Indices: 6227--6265  Score: 51
    Period size: 14  Copynumber: 2.8  Consensus size: 14

       6217 AATAATTTAT

                          
       6227 TATATGATTAAATA
          1 TATATGATTAAATA

              *  *        
       6241 TAAATAATTAAATA
          1 TATATGATTAAATA

                  *    
       6255 TATATGTTTAA
          1 TATATGATTAA

       6266 TAATATTGAA


Statistics
Matches: 20,  Mismatches: 5, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44


Consensus pattern (14 bp):   
TATATGATTAAATA
Done.