Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002166.1 Kokia drynarioides strain JFW-HI SEQ_114122, 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: 7914
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31


Found at i:807 original size:3 final size:3

Alignment explanation


    Indices: 799--838  Score: 80
    Period size: 3  Copynumber: 13.3  Consensus size: 3

        789 TGAAATAAAG

                                                                 
        799 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A

        839 TCCACTAAAG


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   37  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:901 original size:8 final size:8

Alignment explanation


    Indices: 888--913  Score: 52
    Period size: 8  Copynumber: 3.2  Consensus size: 8

        878 ATTACTTAAC

                    
        888 TTACCAAT
          1 TTACCAAT

                    
        896 TTACCAAT
          1 TTACCAAT

                    
        904 TTACCAAT
          1 TTACCAAT

              
        912 TT
          1 TT

        914 GGCCTTATTA


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

Matches are distributed among these distances:
   8   18  1.00

ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42


Consensus pattern (8 bp):   
TTACCAAT

Found at i:7097 original size:37 final size:37

Alignment explanation


    Indices: 7019--7304  Score: 261
    Period size: 37  Copynumber: 7.7  Consensus size: 37

       7009 CACTGGCATA

                              *  *       *** *  *
       7019 AAGCCTGCTAGGCACATAACCCGAATACATTAGTACA
          1 AAGCCTGCTAGGCACATAGCCTGAATACACCGGCACG

                   *           *      *   *      
       7056 AAGCCTGTTAGGCACATAGTCTGAATGCACTGGCACG
          1 AAGCCTGCTAGGCACATAGCCTGAATACACCGGCACG

                      *          **            * 
       7093 AAGCCTGCTAAGCACATAGCCCAAATACACCGGCATG
          1 AAGCCTGCTAGGCACATAGCCTGAATACACCGGCACG

                                         *  *   *
       7130 AAGCCTGCTAGGCACATAGCCTGAATACATCGACACA
          1 AAGCCTGCTAGGCACATAGCCTGAATACACCGGCACG

                        *                         
       7167 AAGCCTGCTAGGAACATAG-CTCGAATACACCGGCACG
          1 AAGCCTGCTAGGCACATAGCCT-GAATACACCGGCACG

                *      *                        *
       7204 AAGCTTGCTAGACACATAGCCTGAATACACCGGCACA
          1 AAGCCTGCTAGGCACATAGCCTGAATACACCGGCACG

                        *    *    *        **  *  
       7241 AAGCCT-CTTAGCCACACAGCCCGAATACACTTGCGCG
          1 AAGCCTGC-TAGGCACATAGCCTGAATACACCGGCACG

                  *       * *          
       7278 AAGCCTACTAGGCATACAGCCTGAATA
          1 AAGCCTGCTAGGCACATAGCCTGAATA

       7305 TTGTGCAACC


Statistics
Matches: 202,  Mismatches: 43, Indels: 8
        0.80            0.17        0.03

Matches are distributed among these distances:
  36    3  0.01
  37  196  0.97
  38    3  0.01

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


Consensus pattern (37 bp):   
AAGCCTGCTAGGCACATAGCCTGAATACACCGGCACG

Found at i:7134 original size:74 final size:74

Alignment explanation


    Indices: 7009--7304  Score: 299
    Period size: 74  Copynumber: 4.0  Consensus size: 74

       6999 ATTCTTGGAT

                    *           *       *          *** *  *       *          
       7009 CACTGGCATAAAGCCTGCTAGGCACATAACCCGAATACATTAGTACAAAGCCTGTTAGGCACATA
          1 CACTGGCACAAAGCCTGCTAAGCACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACATA

             *      *
       7074 GTCTGAATG
         66 GCCTGAATA

                     *                      *            *                   
       7083 CACTGGCACGAAGCCTGCTAAGCACATAGCCCAAATACACCGGCATGAAGCCTGCTAGGCACATA
          1 CACTGGCACAAAGCCTGCTAAGCACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACATA

                     
       7148 GCCTGAATA
         66 GCCTGAATA

                  *              * *       *                    *      *     
       7157 CA-TCGACACAAAGCCTGCTAGGAACATAGCTCGAATACACCGGCACGAAGCTTGCTAGACACAT
          1 CACT-GGCACAAAGCCTGCTAAGCACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACAT

                      
       7221 AGCCTGAATA
         65 AGCCTGAATA

               *               *       *             **  *        *       * *
       7231 CACCGGCACAAAGCCT-CTTAGCCACACAGCCCGAATACACTTGCGCGAAGCCTACTAGGCATAC
          1 CACTGGCACAAAGCCTGCTAAG-CACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACAT

                      
       7295 AGCCTGAATA
         65 AGCCTGAATA

       7305 TTGTGCAACC


Statistics
Matches: 181,  Mismatches: 38, Indels: 6
        0.80            0.17        0.03

Matches are distributed among these distances:
  73    4  0.02
  74  177  0.98

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


Consensus pattern (74 bp):   
CACTGGCACAAAGCCTGCTAAGCACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACATA
GCCTGAATA

Found at i:7207 original size:111 final size:111

Alignment explanation


    Indices: 7013--7269  Score: 315
    Period size: 111  Copynumber: 2.3  Consensus size: 111

       7003 TTGGATCACT

                                    *           *  *          *    *         
       7013 GGCATAAAGCCTGCTAGGCACATAACCCGAATACATTAGTACAAAGCCTGTTAGGCACATAGTCT
          1 GGCATAAAGCCTGCTAGGCACATAGCCCGAATACATGAGCACAAAGCCTGCTAGGAACATAGTCT

                *   *                                      
       7078 GAATGCACTGGCACGAAGCCTGCTA-AGCACATAGCCCAAATACACC
         66 GAATACACCGGCACGAAGCCTGCTAGA-CACATAGCCCAAATACACC

                 *                     *                                     
       7124 GGCATGAAGCCTGCTAGGCACATAGCCTGAATACATCGA-CACAAAGCCTGCTAGGAACATAG-C
          1 GGCATAAAGCCTGCTAGGCACATAGCCCGAATACAT-GAGCACAAAGCCTGCTAGGAACATAGTC

                                 *                **        
       7187 TCGAATACACCGGCACGAAGCTTGCTAGACACATAGCCTGAATACACC
         65 T-GAATACACCGGCACGAAGCCTGCTAGACACATAGCCCAAATACACC

                *             *    *            
       7235 GGCACAAAGCCT-CTTAGCCACACAGCCCGAATACA
          1 GGCATAAAGCCTGC-TAGGCACATAGCCCGAATACA

       7270 CTTGCGCGAA


Statistics
Matches: 125,  Mismatches: 17, Indels: 8
        0.83            0.11        0.05

Matches are distributed among these distances:
 110    3  0.02
 111  120  0.96
 112    2  0.02

ACGTcount: A:0.34, C:0.30, G:0.20, T:0.16


Consensus pattern (111 bp):   
GGCATAAAGCCTGCTAGGCACATAGCCCGAATACATGAGCACAAAGCCTGCTAGGAACATAGTCT
GAATACACCGGCACGAAGCCTGCTAGACACATAGCCCAAATACACC

Done.