Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004486.1 Kokia drynarioides strain JFW-HI SEQ_117912, 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: 30431
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33


Found at i:1525 original size:44 final size:44

Alignment explanation


    Indices: 1458--1569  Score: 134
    Period size: 44  Copynumber: 2.5  Consensus size: 44

       1448 TTCGAGGCAC

                  *           *      *               *  
       1458 AGATAATGCAACGGGGCACAGTTATGGTGACGAGGCAGGTCTAT
          1 AGATAACGCAACGGGGCAAAGTTATAGTGACGAGGCAGGTCCAT

                         *               *     *        
       1502 AGATAACGCAACGTGGCAAAGTTATAGTGGCGAGGTAGGTCCAT
          1 AGATAACGCAACGGGGCAAAGTTATAGTGACGAGGCAGGTCCAT

             *             *  *     
       1546 AAATAACGCAACGGGTCACAGTTA
          1 AGATAACGCAACGGGGCAAAGTTA

       1570 GGGGAGTATG


Statistics
Matches: 57,  Mismatches: 11, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  44   57  1.00

ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20


Consensus pattern (44 bp):   
AGATAACGCAACGGGGCAAAGTTATAGTGACGAGGCAGGTCCAT

Found at i:8535 original size:10 final size:10

Alignment explanation


    Indices: 8520--8549  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       8510 ATTCCTCAAA

                      
       8520 AGTGAAGTGT
          1 AGTGAAGTGT

                    * 
       8530 AGTGAAGTCT
          1 AGTGAAGTGT

                      
       8540 AGTGAAGTGT
          1 AGTGAAGTGT

       8550 GTAAATGAGG


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  10   18  1.00

ACGTcount: A:0.30, C:0.03, G:0.37, T:0.30


Consensus pattern (10 bp):   
AGTGAAGTGT

Found at i:11305 original size:21 final size:20

Alignment explanation


    Indices: 11279--11318  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      11269 ATGGGGTTTG

                      *          
      11279 AATATTATTTGACAATTTTTA
          1 AATATT-TTTCACAATTTTTA

                       *       
      11300 AATATTTTTCATAATTTTT
          1 AATATTTTTCACAATTTTT

      11319 TCTAAGAAAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20   11  0.65
  21    6  0.35

ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57


Consensus pattern (20 bp):   
AATATTTTTCACAATTTTTA

Found at i:21100 original size:116 final size:116

Alignment explanation


    Indices: 20919--21158  Score: 363
    Period size: 116  Copynumber: 2.1  Consensus size: 116

      20909 CATGTATTGG

                                           **                                
      20919 TAGAAGTACAAAGTAAGAGAGAGGTTGTTCATTGACTTGGGCTGTATCGGTAGATGAATAACAAG
          1 TAGAAGTACAAAGTAAGAGAGAGGTTGTTCACCGACTTGGGCTGTATCGGTAGATGAATAACAAG

                    *      *             *     *               
      20984 TATCGGTAGTCATGTGTTTAGAAGTATCGGTAGTTTGCATACTTGTATCGA
         66 TATCGGTAATCATGTATTTAGAAGTATCGATAGTTCGCATACTTGTATCGA

                      **   *             *           *                       
      21035 TAGAAGTACAGGGTAGGAGAGAGGTTGTTTACCGACTTGGGTTGTATCGGTAGATGAATAACAAG
          1 TAGAAGTACAAAGTAAGAGAGAGGTTGTTCACCGACTTGGGCTGTATCGGTAGATGAATAACAAG

               *                                              *
      21100 TATTGGTAATCATGTATTTAGAAGTATCGATAGTTCGCATACTTGTATCGG
         66 TATCGGTAATCATGTATTTAGAAGTATCGATAGTTCGCATACTTGTATCGA

                    
      21151 TAGAAGTA
          1 TAGAAGTA

      21159 GCAGTGTAAG


Statistics
Matches: 111,  Mismatches: 13, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
 116  111  1.00

ACGTcount: A:0.30, C:0.10, G:0.28, T:0.32


Consensus pattern (116 bp):   
TAGAAGTACAAAGTAAGAGAGAGGTTGTTCACCGACTTGGGCTGTATCGGTAGATGAATAACAAG
TATCGGTAATCATGTATTTAGAAGTATCGATAGTTCGCATACTTGTATCGA

Found at i:21234 original size:21 final size:21

Alignment explanation


    Indices: 21210--21264  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 21

      21200 TAGAAATAAA

                            *    
      21210 ACTTGTATCGGTAAAAGAGTC
          1 ACTTGTATCGGTAAAACAGTC

                             *   
      21231 ACTTGTATCGGTAAAACTGTC
          1 ACTTGTATCGGTAAAACAGTC

               *    *    
      21252 ACTGGTATTGGTA
          1 ACTTGTATCGGTA

      21265 GGAATATGTA


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33


Consensus pattern (21 bp):   
ACTTGTATCGGTAAAACAGTC

Found at i:26069 original size:33 final size:33

Alignment explanation


    Indices: 26026--26097  Score: 135
    Period size: 33  Copynumber: 2.2  Consensus size: 33

      26016 TAAGATGCTT

                 *                           
      26026 CAACACACTCGAATTCACATCCTCTTATATTGG
          1 CAACAAACTCGAATTCACATCCTCTTATATTGG

                                             
      26059 CAACAAACTCGAATTCACATCCTCTTATATTGG
          1 CAACAAACTCGAATTCACATCCTCTTATATTGG

                  
      26092 CAACAA
          1 CAACAA

      26098 TGCACATACC


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   38  1.00

ACGTcount: A:0.35, C:0.29, G:0.08, T:0.28


Consensus pattern (33 bp):   
CAACAAACTCGAATTCACATCCTCTTATATTGG

Found at i:29117 original size:30 final size:30

Alignment explanation


    Indices: 29083--29162  Score: 133
    Period size: 30  Copynumber: 2.7  Consensus size: 30

      29073 ACGGTTTTGC

                                     *    
      29083 GAAGGTGGATAATACTGCGGCTCCGGTTGT
          1 GAAGGTGGATAATACTGCGGCTCCGATTGT

                   *         *            
      29113 GAAGGTGAATAATACTGTGGCTCCGATTGT
          1 GAAGGTGGATAATACTGCGGCTCCGATTGT

                                
      29143 GAAGGTGGATAATACTGCGG
          1 GAAGGTGGATAATACTGCGG

      29163 GGAGGTATAG


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  30   45  1.00

ACGTcount: A:0.25, C:0.14, G:0.35, T:0.26


Consensus pattern (30 bp):   
GAAGGTGGATAATACTGCGGCTCCGATTGT
Done.