Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007748.1 Kokia drynarioides strain JFW-HI SEQ_122381, 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: 9065
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:6563 original size:213 final size:213

Alignment explanation


    Indices: 6196--6621  Score: 834
    Period size: 213  Copynumber: 2.0  Consensus size: 213

       6186 AAGCACGTGG

                                                 *                           
       6196 ATCACATGGAAGTAGACTAAAAAACTTAGTAGCAAGTGTTACTTAACAAATCACGACGGTTGGGC
          1 ATCACATGGAAGTAGACTAAAAAACTTAGTAGCAAGTCTTACTTAACAAATCACGACGGTTGGGC

                                                                             
       6261 TTGGCGTGATGGACCGACCTTGAAGTCAATTTCTGCTGACATAAGGTATCCCAAGAAACAGATGA
         66 TTGGCGTGATGGACCGACCTTGAAGTCAATTTCTGCTGACATAAGGTATCCCAAGAAACAGATGA

                *                                                            
       6326 ACATTGGCTTTGTCCATGTCCTTCACTGATATTTTATATTTTGTTGTTTCATCAAGCATTAAAAT
        131 ACATCGGCTTTGTCCATGTCCTTCACTGATATTTTATATTTTGTTGTTTCATCAAGCATTAAAAT

                              
       6391 ATCCCTTCAACCTTCTCT
        196 ATCCCTTCAACCTTCTCT

                                                                             
       6409 ATCACATGGAAGTAGACTAAAAAACTTAGTAGCAAGTCTTACTTAACAAATCACGACGGTTGGGC
          1 ATCACATGGAAGTAGACTAAAAAACTTAGTAGCAAGTCTTACTTAACAAATCACGACGGTTGGGC

                                                                             
       6474 TTGGCGTGATGGACCGACCTTGAAGTCAATTTCTGCTGACATAAGGTATCCCAAGAAACAGATGA
         66 TTGGCGTGATGGACCGACCTTGAAGTCAATTTCTGCTGACATAAGGTATCCCAAGAAACAGATGA

                                                                             
       6539 ACATCGGCTTTGTCCATGTCCTTCACTGATATTTTATATTTTGTTGTTTCATCAAGCATTAAAAT
        131 ACATCGGCTTTGTCCATGTCCTTCACTGATATTTTATATTTTGTTGTTTCATCAAGCATTAAAAT

                              
       6604 ATCCCTTCAACCTTCTCT
        196 ATCCCTTCAACCTTCTCT

       6622 CTATCAAGGG


Statistics
Matches: 211,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 213  211  1.00

ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32


Consensus pattern (213 bp):   
ATCACATGGAAGTAGACTAAAAAACTTAGTAGCAAGTCTTACTTAACAAATCACGACGGTTGGGC
TTGGCGTGATGGACCGACCTTGAAGTCAATTTCTGCTGACATAAGGTATCCCAAGAAACAGATGA
ACATCGGCTTTGTCCATGTCCTTCACTGATATTTTATATTTTGTTGTTTCATCAAGCATTAAAAT
ATCCCTTCAACCTTCTCT

Found at i:7555 original size:24 final size:24

Alignment explanation


    Indices: 7523--7579  Score: 78
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       7513 AATCTTTTAG

                             *      
       7523 TTAAACTCTATTTATTTGTTTCAA
          1 TTAAACTCTATTTATTTATTTCAA

                     *           *  
       7547 TTAAACTCTGTTTATTTATTTGAA
          1 TTAAACTCTATTTATTTATTTCAA

             *       
       7571 TCAAACTCT
          1 TTAAACTCT

       7580 TATTAATCTA


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51


Consensus pattern (24 bp):   
TTAAACTCTATTTATTTATTTCAA

Found at i:8507 original size:22 final size:22

Alignment explanation


    Indices: 8455--8534  Score: 97
    Period size: 23  Copynumber: 3.5  Consensus size: 22

       8445 AAGTACTTAA

                 *                
       8455 CAGTAAGCACACACAGTGCAAT
          1 CAGTAGGCACACACAGTGCAAT

                                   
       8477 CTAGTAGGCACACACAGTGCAAT
          1 C-AGTAGGCACACACAGTGCAAT

                    *    *  *      
       8500 CAGTAGGCGCACATAGCGCAAAT
          1 CAGTAGGCACACACAGTGC-AAT

              *         
       8523 CAATAGGCACAC
          1 CAGTAGGCACAC

       8535 GAGGTACGAA


Statistics
Matches: 50,  Mismatches: 6, Indels: 3
        0.85            0.10        0.05

Matches are distributed among these distances:
  22   16  0.32
  23   34  0.68

ACGTcount: A:0.38, C:0.28, G:0.21, T:0.14


Consensus pattern (22 bp):   
CAGTAGGCACACACAGTGCAAT

Found at i:8567 original size:23 final size:22

Alignment explanation


    Indices: 8453--8576  Score: 86
    Period size: 23  Copynumber: 5.5  Consensus size: 22

       8443 CCAAGTACTT

                           *      
       8453 AACAGTAAGCACACACAGTGCA
          1 AACAGTAAGCACACAAAGTGCA

             *      *       *      
       8475 ATCTAGTAGGCACACACAGTGCA
          1 AAC-AGTAAGCACACAAAGTGCA

             *     *  *    *  *   
       8498 ATCAGTAGGCGCACATAGCGCA
          1 AACAGTAAGCACACAAAGTGCA

                 *  *      * *  *   
       8520 AATCAATAGGCACACGAGGTACGA
          1 AA-CAGTAAGCACACAAAGTGC-A

                                   
       8544 AACAGTAAGCACACAAAGTGCGA
          1 AACAGTAAGCACACAAAGTGC-A

                      
       8567 AACAGTAAGC
          1 AACAGTAAGC

       8577 GCGCTAGCGT


Statistics
Matches: 81,  Mismatches: 18, Indels: 5
        0.78            0.17        0.05

Matches are distributed among these distances:
  22   19  0.23
  23   59  0.73
  24    3  0.04

ACGTcount: A:0.41, C:0.24, G:0.23, T:0.12


Consensus pattern (22 bp):   
AACAGTAAGCACACAAAGTGCA
Done.