Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007562.1 Kokia drynarioides strain JFW-HI SEQ_122190, 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: 15487
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33


Found at i:163 original size:26 final size:26

Alignment explanation


    Indices: 99--239  Score: 151
    Period size: 26  Copynumber: 5.4  Consensus size: 26

         89 GTCAACCAAA

                                  *  * 
         99 CACCGG-TACGAAGCCTGCTATATAAT
          1 CACCGGCT-CGAAGCCTGCTATTTATT

               ***  *                 
        125 CACTATCTTGAAGCCTGCTATTTATT
          1 CACCGGCTCGAAGCCTGCTATTTATT

              *           *           
        151 CATCGGCTCGAAGCTTGCTATTTATT
          1 CACCGGCTCGAAGCCTGCTATTTATT

                                  *    
        177 CACCGGCTC-AAGGCCTGCTATATATT
          1 CACCGGCTCGAA-GCCTGCTATTTATT

                *                     
        203 CACCAGCTCGAAGCCTGCTATTTATT
          1 CACCGGCTCGAAGCCTGCTATTTATT

                 *     
        229 CACCGACTCGA
          1 CACCGGCTCGA

        240 TTCACTTATT


Statistics
Matches: 93,  Mismatches: 19, Indels: 6
        0.79            0.16        0.05

Matches are distributed among these distances:
  25    2  0.02
  26   88  0.95
  27    3  0.03

ACGTcount: A:0.24, C:0.28, G:0.17, T:0.30


Consensus pattern (26 bp):   
CACCGGCTCGAAGCCTGCTATTTATT

Found at i:5527 original size:26 final size:26

Alignment explanation


    Indices: 5489--5696  Score: 181
    Period size: 26  Copynumber: 8.0  Consensus size: 26

       5479 GCCAACCAAA

                   *                * 
       5489 CACCGGCACGAAGCCTGCTATATAAT
          1 CACCGGCTCGAAGCCTGCTATATATT

               *    *            *    
       5515 CACTGGCTTGAAGCCTGCTATTTATT
          1 CACCGGCTCGAAGCCTGCTATATATT

              *           *      *    
       5541 CATCGGCTCGAAGCTTGCTATTTATT
          1 CACCGGCTCGAAGCCTGCTATATATT

                 *                     
       5567 CACCGACTC-AAGGCCTGCTATATATT
          1 CACCGGCTCGAA-GCCTGCTATATATT

                *                *    
       5593 CACCAGCTCGAAGCCTGCTATTTATT
          1 CACCGGCTCGAAGCCTGCTATATATT

              * *         * *        * 
       5619 CATCAGCTCGAAGCTTACTA-ATTACT
          1 CACCGGCTCGAAGCCTGCTATA-TATT

                             *         
       5645 CACCGGCTC-AAGGCCTACTATATATT
          1 CACCGGCTCGAA-GCCTGCTATATATT

                      *           *    
       5671 CA-CGCGCTCAAAGCCTGCTATTTATT
          1 CACCG-GCTCGAAGCCTGCTATATATT

       5697 TGTTTACAAA


Statistics
Matches: 148,  Mismatches: 27, Indels: 14
        0.78            0.14        0.07

Matches are distributed among these distances:
  25    6  0.04
  26  137  0.93
  27    5  0.03

ACGTcount: A:0.25, C:0.28, G:0.16, T:0.30


Consensus pattern (26 bp):   
CACCGGCTCGAAGCCTGCTATATATT

Found at i:5606 original size:78 final size:77

Alignment explanation


    Indices: 5501--5696  Score: 275
    Period size: 78  Copynumber: 2.5  Consensus size: 77

       5491 CCGGCACGAA

                        *     *   *                     *           *   *   *
       5501 GCCTGCTATATAATCACTGGCTTGAAGCCTGCTATTTATTCATCGGCTCGAAGCTTGCTATTTAT
          1 GCCTGCTATATATTCAC-CGCTCGAAGCCTGCTATTTATTCATCAGCTCGAAGCTTACTAATTAC

                         
       5566 TCACCGACTCAAG
         65 TCACCGACTCAAG

                                                                             
       5579 GCCTGCTATATATTCACCAGCTCGAAGCCTGCTATTTATTCATCAGCTCGAAGCTTACTAATTAC
          1 GCCTGCTATATATTCACC-GCTCGAAGCCTGCTATTTATTCATCAGCTCGAAGCTTACTAATTAC

                  *      
       5644 TCACCGGCTCAAG
         65 TCACCGACTCAAG

                *                  *                
       5657 GCCTACTATATATTCACGCGCTCAAAGCCTGCTATTTATT
          1 GCCTGCTATATATTCAC-CGCTCGAAGCCTGCTATTTATT

       5697 TGTTTACAAA


Statistics
Matches: 106,  Mismatches: 10, Indels: 4
        0.88            0.08        0.03

Matches are distributed among these distances:
  78  105  0.99
  79    1  0.01

ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32


Consensus pattern (77 bp):   
GCCTGCTATATATTCACCGCTCGAAGCCTGCTATTTATTCATCAGCTCGAAGCTTACTAATTACT
CACCGACTCAAG

Found at i:9008 original size:21 final size:21

Alignment explanation


    Indices: 8969--9008  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       8959 ACATTTTTCT

                                 
       8969 TACTCTTTTCTTTTGTGTTTG
          1 TACTCTTTTCTTTTGTGTTTG

                                
       8990 TACTCATTTTCTTTT-TGTT
          1 TACTC-TTTTCTTTTGTGTT

       9009 CTTTTCACTT


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

Matches are distributed among these distances:
  21    9  0.50
  22    9  0.50

ACGTcount: A:0.07, C:0.15, G:0.10, T:0.68


Consensus pattern (21 bp):   
TACTCTTTTCTTTTGTGTTTG
Done.