Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011093.1 Kokia drynarioides strain JFW-HI SEQ_126066, 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: 2181
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25


Found at i:1297 original size:49 final size:49

Alignment explanation


    Indices: 1235--1655  Score: 450
    Period size: 49  Copynumber: 8.6  Consensus size: 49

       1225 GTACCGTGAA

                                          *              *   
       1235 ACATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACCAAG
          1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAG

             *   *        **     *       *              *      
       1284 ATATGGAGGGAAAGGCTTAAGTCGCAACGACGAA-CCATGTACCTCAGAAG
          1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA-GTACCAC-GAAG

                                  *            * *            
       1334 ACATGAAGGGAAAGATTTAAGCTGCAACGGCGAATTCGGTACCAC-AGAG
          1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGA-AG

              * *                  *   * *      *        *   
       1383 ACGTAAAGGGAAAGATTTAAGCCACAATGACGAATCTAGTACCACAAAG
          1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAG

               *   *                       *      *          
       1432 ACACGAATGGAAAGATTTAAGCCGCAACGGCAAATCCACTACCACGAAG
          1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAG

                            *               *                
       1481 ACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAG
          1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAG

               **         *      * *          *        *     
       1530 ACACAAAGGGAAAGGTTTAAGTCACAACGGCGAACCCAGTACCTCGAAG
          1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAG

                                       *                    *
       1579 ACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAA
          1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAG

             * *  *          *    *     
       1628 ATACGAGGGGAAAGATTGAAGCGGCAAC
          1 ACATGAAGGGAAAGATTTAAGCCGCAAC

       1656 AGCAAATCTA


Statistics
Matches: 298,  Mismatches: 69, Indels: 10
        0.79            0.18        0.03

Matches are distributed among these distances:
  48    4  0.01
  49  256  0.86
  50   37  0.12
  51    1  0.00

ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14


Consensus pattern (49 bp):   
ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAG

Found at i:2052 original size:11 final size:11

Alignment explanation


    Indices: 2036--2087  Score: 52
    Period size: 11  Copynumber: 4.7  Consensus size: 11

       2026 AGCCTTTGGT

                       
       2036 TTTAAATTAGG
          1 TTTAAATTAGG

                       
       2047 TTTAAATT-GG
          1 TTTAAATTAGG

                      **
       2057 TTTAAATTTATT
          1 TTTAAA-TTAGG

                     **
       2069 TTTAAATTAAA
          1 TTTAAATTAGG

                    
       2080 TTTAAATT
          1 TTTAAATT

       2088 TATCTTTTTA


Statistics
Matches: 35,  Mismatches: 4, Indels: 4
        0.81            0.09        0.09

Matches are distributed among these distances:
  10    8  0.23
  11   21  0.60
  12    6  0.17

ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54


Consensus pattern (11 bp):   
TTTAAATTAGG

Found at i:2060 original size:10 final size:10

Alignment explanation


    Indices: 2031--2064  Score: 50
    Period size: 10  Copynumber: 3.2  Consensus size: 10

       2021 GATCAAGCCT

                       
       2031 TTGGTTTTAAA
          1 TTGG-TTTAAA

                       
       2042 TTAGGTTTAAA
          1 TT-GGTTTAAA

                      
       2053 TTGGTTTAAA
          1 TTGGTTTAAA

              
       2063 TT
          1 TT

       2065 TATTTTTAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  10   10  0.45
  11   10  0.45
  12    2  0.09

ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53


Consensus pattern (10 bp):   
TTGGTTTAAA

Found at i:2130 original size:16 final size:16

Alignment explanation


    Indices: 2094--2131  Score: 58
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       2084 AATTTATCTT

                          * 
       2094 TTTAAATTTGAATTTA
          1 TTTAAATTTGAATTGA

            *               
       2110 ATTAAATTTGAATTGA
          1 TTTAAATTTGAATTGA

                  
       2126 TTTAAA
          1 TTTAAA

       2132 ACTTAATATT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50


Consensus pattern (16 bp):   
TTTAAATTTGAATTGA
Done.