Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006738.1 Kokia drynarioides strain JFW-HI SEQ_121336, 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: 6768
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:2120 original size:25 final size:25

Alignment explanation


    Indices: 2086--2162  Score: 118
    Period size: 25  Copynumber: 3.1  Consensus size: 25

       2076 ATACTGGTTA

                *          *         
       2086 AACTTTATCTGGGCTTGTAAGAGCT
          1 AACTCTATCTGGGCTCGTAAGAGCT

                                     
       2111 AACTCTATCTGGGCTCGTAAGAGCT
          1 AACTCTATCTGGGCTCGTAAGAGCT

                             * *     
       2136 AACTCTATCTGGGCTCGCATGAGCT
          1 AACTCTATCTGGGCTCGTAAGAGCT

              
       2161 AA
          1 AA

       2163 ATTTCTAGAA


Statistics
Matches: 48,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   48  1.00

ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30


Consensus pattern (25 bp):   
AACTCTATCTGGGCTCGTAAGAGCT

Found at i:4828 original size:69 final size:70

Alignment explanation


    Indices: 4699--4828  Score: 165
    Period size: 69  Copynumber: 1.9  Consensus size: 70

       4689 CCTACGCTTA

                                 *    *         *                  *         
       4699 CAACTGATATCATAAAGGTTTTGCCGGATTAAGAATGCAACCTCCAAAACAACTAGCGAACTTAC
          1 CAACTGATATCATAAAGGTTTCGCCGAATTAAGAATACAACCTCCAAAACAACTAACGAACTTAC

                 
       4764 AATCC
         66 AATCC

                    *                          *              * *         
       4769 CAACTGATGTCATAAAGG-TTCGCC-AATTTAAGATTACAACCTCCAAAATAGCTAACGAAC
          1 CAACTGATATCATAAAGGTTTCGCCGAA-TTAAGAATACAACCTCCAAAACAACTAACGAAC

       4829 CTATGTTCCC


Statistics
Matches: 51,  Mismatches: 8, Indels: 3
        0.82            0.13        0.05

Matches are distributed among these distances:
  68    1  0.02
  69   33  0.65
  70   17  0.33

ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23


Consensus pattern (70 bp):   
CAACTGATATCATAAAGGTTTCGCCGAATTAAGAATACAACCTCCAAAACAACTAACGAACTTAC
AATCC

Found at i:4989 original size:68 final size:69

Alignment explanation


    Indices: 4909--5037  Score: 179
    Period size: 69  Copynumber: 1.9  Consensus size: 69

       4899 ACACTCTCAG

                                      *                        *             
       4909 TTGATGTCATAAA-GGTTCACCGATTGATATCGCAACCTCCAAAATAGCTATCGGACCTACGCTC
          1 TTGATGTCATAAATGGTTCACCGATTAATATCGCAACCTCCAAAATAGCTAGCGGACCTACGCTC

                
       4973 CCAA
         66 CCAA

                 *         *  ** * *                                     
       4977 TTGATTTCATAAATGTTTGTCGGTTTAATATCGCAACCTCCAAAATAGCTAGCGGACCTAC
          1 TTGATGTCATAAATGGTTCACCGATTAATATCGCAACCTCCAAAATAGCTAGCGGACCTAC

       5038 ATTCCCAGCT


Statistics
Matches: 52,  Mismatches: 8, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  68   12  0.23
  69   40  0.77

ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29


Consensus pattern (69 bp):   
TTGATGTCATAAATGGTTCACCGATTAATATCGCAACCTCCAAAATAGCTAGCGGACCTACGCTC
CCAA
Done.