Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008657.1 Kokia drynarioides strain JFW-HI SEQ_123338, 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: 7952
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:568 original size:13 final size:13

Alignment explanation


    Indices: 536--576  Score: 50
    Period size: 12  Copynumber: 3.3  Consensus size: 13

        526 TTTCCAATAA

                         
        536 ATTTCAA-TTTTT
          1 ATTTCAATTTTTT

            *            
        548 GTTT-AATTTTTT
          1 ATTTCAATTTTTT

                       * 
        560 ATTTCAATTTTAT
          1 ATTTCAATTTTTT

                
        573 ATTT
          1 ATTT

        577 TAACTTAATA


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  11    2  0.08
  12   11  0.46
  13   11  0.46

ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68


Consensus pattern (13 bp):   
ATTTCAATTTTTT

Found at i:3992 original size:82 final size:82

Alignment explanation


    Indices: 3850--4004  Score: 195
    Period size: 82  Copynumber: 1.9  Consensus size: 82

       3840 ACGTTTTTCT

                *             *    *                         *     *         
       3850 TTGATAGCGTTTTACTGGTACCATGCGAAAAGCACTTCCAACTAAAAGCTTTTTTTTGCATTCCA
          1 TTGAAAGCGTTTTACTGGCACCACGCGAAAAGCACTTCCAACTAAAAGCATTTTTCTGCATTCCA

               *             
       3915 CTTGAAAATGCTTCCAA
         66 CTTAAAAATGCTTCCAA

                          *      *     *            *                      * 
       3932 TTGAAAGCGTTTTATTGGCACTACGCGGAAAGCACTTCCAGCTAGAAA-CATTTTTCTGCATTTC
          1 TTGAAAGCGTTTTACTGGCACCACGCGAAAAGCACTTCCAACTA-AAAGCATTTTTCTGCATTCC

                     
       3996 ACTTAAAAA
         65 ACTTAAAAA

       4005 CACTTTCACC


Statistics
Matches: 61,  Mismatches: 11, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  82   58  0.95
  83    3  0.05

ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33


Consensus pattern (82 bp):   
TTGAAAGCGTTTTACTGGCACCACGCGAAAAGCACTTCCAACTAAAAGCATTTTTCTGCATTCCA
CTTAAAAATGCTTCCAA

Found at i:4019 original size:82 final size:82

Alignment explanation


    Indices: 3855--4028  Score: 188
    Period size: 82  Copynumber: 2.1  Consensus size: 82

       3845 TTTCTTTGAT

                         *    *                         *     *            * 
       3855 AGCGTTTTACTGGTACCATGCGAAAAGCACTTCCAACTAAAAGCTTTTTTTTGCATTCCACTTGA
          1 AGCGTTTTACTGGCACCACGCGAAAAGCACTTCCAACTAAAAGCATTTTTCTGCATTCCACTTAA

               **       *    
       3920 AAATGCTTCCAATTGAA
         66 AAACACTTCCAACTGAA

                     *      *     *            *                      *      
       3937 AGCGTTTTATTGGCACTACGCGGAAAGCACTTCCAGCTAGAAA-CATTTTTCTGCATTTCACTTA
          1 AGCGTTTTACTGGCACCACGCGAAAAGCACTTCCAACTA-AAAGCATTTTTCTGCATTCCACTTA

                     *  *     
       4001 AAAACACTTTCACCTGAA
         65 AAAACACTTCCAACTGAA

                      
       4019 AGCGATTTTA
          1 AGCG-TTTTA

       4029 AATTATCGAC


Statistics
Matches: 75,  Mismatches: 15, Indels: 3
        0.81            0.16        0.03

Matches are distributed among these distances:
  82   67  0.89
  83    8  0.11

ACGTcount: A:0.30, C:0.22, G:0.15, T:0.32


Consensus pattern (82 bp):   
AGCGTTTTACTGGCACCACGCGAAAAGCACTTCCAACTAAAAGCATTTTTCTGCATTCCACTTAA
AAACACTTCCAACTGAA
Done.