Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012142.1 Kokia drynarioides strain JFW-HI SEQ_127141, 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: 19842
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:2475 original size:22 final size:22

Alignment explanation


    Indices: 2440--2494  Score: 58
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       2430 AGACACAGCC

                           * *     
       2440 TTTATTATAA-ATATTATTTTTA
          1 TTTATTA-AATATATAAGTTTTA

                                  
       2462 TTTATTAAATATATAAGTTTTA
          1 TTTATTAAATATATAAGTTTTA

              *        
       2484 TAATATTAAAT
          1 T-TTATTAAAT

       2495 TACGAAATTA


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  21    2  0.07
  22   18  0.64
  23    8  0.29

ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56


Consensus pattern (22 bp):   
TTTATTAAATATATAAGTTTTA

Found at i:8992 original size:33 final size:33

Alignment explanation


    Indices: 8950--9016  Score: 134
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       8940 CCAAGTCCTA

                                             
       8950 AAACTACACCTGAGCCCACTAAAACCAATGCAC
          1 AAACTACACCTGAGCCCACTAAAACCAATGCAC

                                             
       8983 AAACTACACCTGAGCCCACTAAAACCAATGCAC
          1 AAACTACACCTGAGCCCACTAAAACCAATGCAC

             
       9016 A
          1 A

       9017 CATGCCCAAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.43, C:0.36, G:0.09, T:0.12


Consensus pattern (33 bp):   
AAACTACACCTGAGCCCACTAAAACCAATGCAC

Found at i:17762 original size:98 final size:97

Alignment explanation


    Indices: 17593--17936  Score: 401
    Period size: 98  Copynumber: 3.5  Consensus size: 97

      17583 GTTTCATTAC

                                  *                                       *  
      17593 CATGAAGGGAAAGATTTAAGCCACAACGGCGAATCTAGTACCACGAAGACACAAAGGAAAAGATT
          1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACACAAAGG-AAAGGTT

                         *                   
      17658 TAAGTCGTAATAGTGAACCTTGTACCTTAGAAG
         65 TAAGTCGTAATAGAGAACCTTGTACCTTAGAAG

                               *      *                                      
      17691 CATGAAGGGAAAGATTTAAACCGCAATGGCGAATCTAGTACCACGAAGACACAAATGGAAAGGTT
          1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACACAAA-GGAAAGGTT

                   *   * *       *         * 
      17756 TAAGTCGCAATGGCGAA-CTTATACCTTAGAGG
         65 TAAGTCGTAATAGAGAACCTTGTACCTTAGAAG

               *   *                           * *           *          *    
      17788 CATTAAGTGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATACAAAAGGAATGGTT
          1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACAC-AAAGGAAAGGTT

                                   *       *     
      17853 TAAG-C-TACA-ACGAAGAACCTAGTACC-TCGAAAG
         65 TAAGTCGTA-ATA-G-AGAACCTTGTACCTTAG-AAG

              *                    *                  *        
      17886 CACGAAGGGAAAGATTTAAGCCGTAACGGCGAATCTAGTACCGCGAAGACA
          1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACA

      17937 TTATAGTCAC


Statistics
Matches: 207,  Mismatches: 32, Indels: 14
        0.82            0.13        0.06

Matches are distributed among these distances:
  95    1  0.00
  96    3  0.01
  97   75  0.36
  98  126  0.61
  99    2  0.01

ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18


Consensus pattern (97 bp):   
CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACACAAAGGAAAGGTTT
AAGTCGTAATAGAGAACCTTGTACCTTAGAAG

Found at i:17926 original size:49 final size:50

Alignment explanation


    Indices: 17597--17936  Score: 225
    Period size: 49  Copynumber: 7.0  Consensus size: 50

      17587 CATTACCATG

                              *                               
      17597 AAGGGAAAGATTTAAGCCACAACGGCGAATCTAGTACCACG-AAGACACA
          1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAAGACACA

                *           *  *  ** *   *  *                 **
      17646 AAGGAAAAGATTTAAGTCGTAATAGTGAACCTTGTACCTTA-G-AAG-CATG
          1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACC--ACGAAAGACACA

                           *      *                           
      17695 AAGGGAAAGATTTAAACCGCAATGGCGAATCTAGTACCACG-AAGACACA
          1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAAGACACA

              *      *      *     *                 ** *  *  **
      17744 AATGGAAAGGTTTAAGTCGCAATGGCGAA-CTTA-TACC-TTAGAGGCATT
          1 AAGGGAAAGATTTAAGCCGCAACGGCGAATC-TAGTACCACGAAAGACACA

               *                           * *            *   
      17792 AAGTGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACG-AAGATACA
          1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAAGACACA

              *    * *       **     **   *        *          *
      17841 AAAGGAATGGTTTAAGCTACAACGAAGAACCTAGTACCTCGAAAG-CACG
          1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAAGACACA

                               *                  *         
      17890 AAGGGAAAGATTTAAGCCGTAACGGCGAATCTAGTACCGCG-AAGACA
          1 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAAGACA

      17937 TTATAGTCAC


Statistics
Matches: 212,  Mismatches: 68, Indels: 22
        0.70            0.23        0.07

Matches are distributed among these distances:
  47    1  0.00
  48   41  0.19
  49  162  0.76
  50    7  0.03
  51    1  0.00

ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18


Consensus pattern (50 bp):   
AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAAGACACA
Done.