Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002851.1 Kokia drynarioides strain JFW-HI SEQ_115243, 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: 22687
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:6972 original size:29 final size:31

Alignment explanation


    Indices: 6915--6973  Score: 86
    Period size: 29  Copynumber: 2.0  Consensus size: 31

       6905 GACTTGAGTT

                             *             
       6915 TTGAAATATAAAAAGTAGAGAGATTAAATTC
          1 TTGAAATATAAAAAGTACAGAGATTAAATTC

                       *                  
       6946 TTGAAA-ATAAGAA-TACAGAGATTAAATT
          1 TTGAAATATAAAAAGTACAGAGATTAAATT

       6974 TCAAATTTGT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  29   14  0.54
  30    6  0.23
  31    6  0.23

ACGTcount: A:0.53, C:0.03, G:0.15, T:0.29


Consensus pattern (31 bp):   
TTGAAATATAAAAAGTACAGAGATTAAATTC

Found at i:14185 original size:13 final size:13

Alignment explanation


    Indices: 14167--14191  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      14157 AAATATATTT

                         
      14167 ATTAATTAAAAAC
          1 ATTAATTAAAAAC

                        
      14180 ATTAATTAAAAA
          1 ATTAATTAAAAA

      14192 AAAGAAGAAG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32


Consensus pattern (13 bp):   
ATTAATTAAAAAC

Found at i:16063 original size:159 final size:159

Alignment explanation


    Indices: 15774--16088  Score: 477
    Period size: 159  Copynumber: 2.0  Consensus size: 159

      15764 TTACGTAGCT

                     *                                                *      
      15774 TTGGCAATGTAGAAAACAATCTTGAATACCTTGCCTTCAACGGATCCTGCATCAACGATGGTCTA
          1 TTGGCAATGGAGAAAACAATCTTGAATACCTTGCCTTCAACGGATCCTGCATCAACGACGGTCTA

              *        *   *              *        **              *         
      15839 TCGATTGTACTGGTATGGTTGAAACCAAAATTAGAGCTGTGGAGCGGTGTTGCCATCTGTGAATC
         66 TCCATTGTACTAGTACGGTTGAAACCAAAAGTAGAGCTGCAGAGCGGTGTTGCCAACTGTGAATC

                                         
      15904 TGGCCGGAAGCTGGCGATTGATACTCCCC
        131 TGGCCGGAAGCTGGCGATTGATACTCCCC

                                                  **     *                   
      15933 TTGGCAATGGAGAAAACAATCTTGAATACCTTGCCTTCCTCGGATTCTGCATCAACGACGGTCTA
          1 TTGGCAATGGAGAAAACAATCTTGAATACCTTGCCTTCAACGGATCCTGCATCAACGACGGTCTA

                                       *                        *   *        
      15998 TCCATTGTACTAGTACGGTTGAAACCAGAAGTAGAGCTGCAGAGCGGTGTTGTCAAGTGTGAATC
         66 TCCATTGTACTAGTACGGTTGAAACCAAAAGTAGAGCTGCAGAGCGGTGTTGCCAACTGTGAATC

                *     *               
      16063 TGGCTGGAAGGTGGCGATTGATACTC
        131 TGGCCGGAAGCTGGCGATTGATACTC

      16089 GCTTTTTAGG


Statistics
Matches: 139,  Mismatches: 17, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
 159  139  1.00

ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27


Consensus pattern (159 bp):   
TTGGCAATGGAGAAAACAATCTTGAATACCTTGCCTTCAACGGATCCTGCATCAACGACGGTCTA
TCCATTGTACTAGTACGGTTGAAACCAAAAGTAGAGCTGCAGAGCGGTGTTGCCAACTGTGAATC
TGGCCGGAAGCTGGCGATTGATACTCCCC

Found at i:21300 original size:23 final size:23

Alignment explanation


    Indices: 21274--21348  Score: 82
    Period size: 23  Copynumber: 3.3  Consensus size: 23

      21264 AAAATTAAAC

                                   
      21274 TATAATTTTTATGATAGTAAAAA
          1 TATAATTTTTATGATAGTAAAAA

                    ** *      *   *
      21297 TATAATTTGGAGGA-A-TTAAAC
          1 TATAATTTTTATGATAGTAAAAA

                                   
      21318 TATAATTTTTATGATAGTAAAAA
          1 TATAATTTTTATGATAGTAAAAA

              *     
      21341 TACAATTT
          1 TATAATTT

      21349 CAATATTTTA


Statistics
Matches: 39,  Mismatches: 11, Indels: 4
        0.72            0.20        0.07

Matches are distributed among these distances:
  21   15  0.38
  22    2  0.05
  23   22  0.56

ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41


Consensus pattern (23 bp):   
TATAATTTTTATGATAGTAAAAA
Done.