Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007370.1 Kokia drynarioides strain JFW-HI SEQ_121986, 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: 14081
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:2188 original size:21 final size:21

Alignment explanation


    Indices: 2159--2202  Score: 61
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2149 AATGTGTCTA

                          * *    
       2159 AATTATATTTTATATTTATTT
          1 AATTATATTTTATAGTGATTT

                *                
       2180 AATTCTATTTTATAGTGATTT
          1 AATTATATTTTATAGTGATTT

              
       2201 AA
          1 AA

       2203 ATATGTAATT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59


Consensus pattern (21 bp):   
AATTATATTTTATAGTGATTT

Found at i:3681 original size:19 final size:19

Alignment explanation


    Indices: 3659--3703  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       3649 TTATATTAGG

                                
       3659 ATTTAATATTTAAGATAT-T
          1 ATTTAATATTTAA-ATATGT

                 *         *   
       3678 ATTTATTATTTAAATTTGT
          1 ATTTAATATTTAAATATGT

                   
       3697 ATTTAAT
          1 ATTTAAT

       3704 TTATGCTTAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  18    3  0.14
  19   19  0.86

ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58


Consensus pattern (19 bp):   
ATTTAATATTTAAATATGT

Found at i:7941 original size:51 final size:51

Alignment explanation


    Indices: 7865--7965  Score: 193
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       7855 TGGTGTACTG

                                                               
       7865 AAGGGTAGGGCGGTTGAGTGGTGTGGACTTTTTAAAAAAAAGAACCTATTA
          1 AAGGGTAGGGCGGTTGAGTGGTGTGGACTTTTTAAAAAAAAGAACCTATTA

                    *                                         
       7916 AAGGGTAGTGCGGTTGAGTGGTGTGGACTTTTTAAAAAAAAGAACCTATT
          1 AAGGGTAGGGCGGTTGAGTGGTGTGGACTTTTTAAAAAAAAGAACCTATT

       7966 GGTCTACTGG


Statistics
Matches: 49,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  51   49  1.00

ACGTcount: A:0.33, C:0.08, G:0.31, T:0.29


Consensus pattern (51 bp):   
AAGGGTAGGGCGGTTGAGTGGTGTGGACTTTTTAAAAAAAAGAACCTATTA

Found at i:14006 original size:23 final size:23

Alignment explanation


    Indices: 13975--14070  Score: 104
    Period size: 23  Copynumber: 4.2  Consensus size: 23

      13965 TGGGCAACAG

                      *             
      13975 AGAGCACACACAGTGCTAAATAA-
          1 AGAGCACACAAAGTGCT-AATAAC

                *         *   * * *
      13998 AGAGTACACAAAGTACTAGTCAG
          1 AGAGCACACAAAGTGCTAATAAC

                                  *
      14021 AGAGCACACAAAGTGCTAATAAG
          1 AGAGCACACAAAGTGCTAATAAC

                      *            
      14044 AGAGCACACACAGTGCTAATAAC
          1 AGAGCACACAAAGTGCTAATAAC

                
      14067 AGAG
          1 AGAG

      14071 AGCACGAGAC


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

Matches are distributed among these distances:
  22    3  0.05
  23   58  0.95

ACGTcount: A:0.46, C:0.20, G:0.21, T:0.14


Consensus pattern (23 bp):   
AGAGCACACAAAGTGCTAATAAC

Done.