Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011416.1 Kokia drynarioides strain JFW-HI SEQ_126399, 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: 13892
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34


Found at i:1607 original size:16 final size:16

Alignment explanation


    Indices: 1586--1619  Score: 68
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1576 TTCATCCTCG

                            
       1586 AAATTTACCTACACTA
          1 AAATTTACCTACACTA

                            
       1602 AAATTTACCTACACTA
          1 AAATTTACCTACACTA

              
       1618 AA
          1 AA

       1620 CAATTGTGGA


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

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29


Consensus pattern (16 bp):   
AAATTTACCTACACTA

Found at i:6985 original size:21 final size:23

Alignment explanation


    Indices: 6960--7103  Score: 170
    Period size: 23  Copynumber: 6.3  Consensus size: 23

       6950 GGAACAAACG

                 *                 
       6960 GAGAGTAC-CAAAGTACTAA-CA
          1 GAGAGCACACAAAGTACTAATCA

                       *   *    *  
       6981 GAGAGCACACACAGTGCTAAACA
          1 GAGAGCACACAAAGTACTAATCA

                 *                 
       7004 GAGAGTACACAAAGTACTAATCA
          1 GAGAGCACACAAAGTACTAATCA

                                   
       7027 GAGAGCACACAAAGTACTAATCA
          1 GAGAGCACACAAAGTACTAATCA

                           *       
       7050 GAGAG--CACAAAGTGCTAATCA
          1 GAGAGCACACAAAGTACTAATCA

                       *   *         
       7071 GAGAGCACACACAGTGCTAATAACA
          1 GAGAGCACACAAAGTACTAAT--CA

                    
       7096 GAGAGCAC
          1 GAGAGCAC

       7104 GAGACGTGCT


Statistics
Matches: 107,  Mismatches: 10, Indels: 8
        0.86            0.08        0.06

Matches are distributed among these distances:
  21   27  0.25
  22    9  0.08
  23   61  0.57
  25   10  0.09

ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12


Consensus pattern (23 bp):   
GAGAGCACACAAAGTACTAATCA

Found at i:7004 original size:23 final size:23

Alignment explanation


    Indices: 6977--7124  Score: 167
    Period size: 23  Copynumber: 6.4  Consensus size: 23

       6967 CCAAAGTACT

                                   
       6977 AACAGAGAGCACACACAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

                     *     *   *   
       7000 AACAGAGAGTACACAAAGTACTA
          1 AACAGAGAGCACACACAGTGCTA

             *             *   *   
       7023 ATCAGAGAGCACACAAAGTACTA
          1 AACAGAGAGCACACACAGTGCTA

             *                     
       7046 ATCAGAGAGCACA-A-AGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

             *                      
       7067 ATCAGAGAGCACACACAGTGCTAA
          1 AACAGAGAGCACACACAGTGCT-A

                           *         
       7091 TAACAGAGAGCACGAGAC-GTGCTA
          1 -AACAGAGAGCAC-ACACAGTGCTA

                      
       7115 AACAGAGAGC
          1 AACAGAGAGC

       7125 GTGCTAGTGT


Statistics
Matches: 112,  Mismatches: 8, Indels: 10
        0.86            0.06        0.08

Matches are distributed among these distances:
  21   19  0.17
  22    2  0.02
  23   70  0.62
  24    2  0.02
  25   16  0.14
  26    3  0.03

ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11


Consensus pattern (23 bp):   
AACAGAGAGCACACACAGTGCTA

Found at i:7036 original size:44 final size:45

Alignment explanation


    Indices: 6955--7100  Score: 174
    Period size: 44  Copynumber: 3.2  Consensus size: 45

       6945 TATACGGAAC

                *                                         
       6955 AAACGGAGAGTAC-CAAAGTACTAA-CAGAGAGCACACACAGTGCT
          1 AAACAGAGAGTACACAAAGTACTAATCAGAGAG-ACACACAGTGCT

                                                   *   *  
       6999 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTACT
          1 AAACAGAGAGTACACAAAGTACTAATCAGAGAG-ACACACAGTGCT

              *                 *                         
       7045 AATCAGAGAG--CACAAAGTGCTAATCAGAGAGCACACACAGTGCT
          1 AAACAGAGAGTACACAAAGTACTAATCAGAGAG-ACACACAGTGCT

                        
       7089 AATAACAGAGAG
          1 -A-AACAGAGAG

       7101 CACGAGACGT


Statistics
Matches: 90,  Mismatches: 8, Indels: 6
        0.87            0.08        0.06

Matches are distributed among these distances:
  44   43  0.48
  45   12  0.13
  46   35  0.39

ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12


Consensus pattern (45 bp):   
AAACAGAGAGTACACAAAGTACTAATCAGAGAGACACACAGTGCT

Found at i:7101 original size:46 final size:46

Alignment explanation


    Indices: 6968--7103  Score: 192
    Period size: 46  Copynumber: 3.0  Consensus size: 46

       6958 CGGAGAGTAC

                                                            
       6968 CAAAGTACTAA-CAGAGAGCACACACAGTGCT-A-AACAGAGAGTACA
          1 CAAAGTACTAATCAGAGAGCACACACAGTGCTAATAACAGAGAG--CA

                                     *   *                
       7013 CAAAGTACTAATCAGAGAGCACACAAAGTACTAAT--CAGAGAGCA
          1 CAAAGTACTAATCAGAGAGCACACACAGTGCTAATAACAGAGAGCA

                  *                                       
       7057 CAAAGTGCTAATCAGAGAGCACACACAGTGCTAATAACAGAGAGCA
          1 CAAAGTACTAATCAGAGAGCACACACAGTGCTAATAACAGAGAGCA

             
       7103 C
          1 C

       7104 GAGACGTGCT


Statistics
Matches: 81,  Mismatches: 5, Indels: 9
        0.85            0.05        0.09

Matches are distributed among these distances:
  44   34  0.42
  45   11  0.14
  46   35  0.43
  47    1  0.01

ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12


Consensus pattern (46 bp):   
CAAAGTACTAATCAGAGAGCACACACAGTGCTAATAACAGAGAGCA
Done.