Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001456.1 Kokia drynarioides strain JFW-HI SEQ_112975, 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: 31287
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:726 original size:12 final size:13

Alignment explanation


    Indices: 704--737  Score: 54
    Period size: 12  Copynumber: 2.8  Consensus size: 13

        694 ATTTATATTT

                         
        704 ATAAAAT-AATAA
          1 ATAAAATAAATAA

                         
        716 AT-AAATAAATAA
          1 ATAAAATAAATAA

                      
        728 ATAAAATAAA
          1 ATAAAATAAA

        738 ATGAGTTTTT


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

Matches are distributed among these distances:
  11    4  0.20
  12    9  0.45
  13    7  0.35

ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24


Consensus pattern (13 bp):   
ATAAAATAAATAA

Found at i:14519 original size:3 final size:3

Alignment explanation


    Indices: 14511--14567  Score: 64
    Period size: 3  Copynumber: 19.0  Consensus size: 3

      14501 GTATTAAAGC

                                                  *                      
      14511 AGA AGA AGA AGAA AGA A-A AGA AGA AGA AAA AGA AG- AGA AGGA AGA
          1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA

             *             
      14556 AAA AGA AGA AGA
          1 AGA AGA AGA AGA

      14568 CGTTGCCCCG


Statistics
Matches: 46,  Mismatches: 4, Indels: 8
        0.79            0.07        0.14

Matches are distributed among these distances:
   2    4  0.09
   3   36  0.78
   4    6  0.13

ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00


Consensus pattern (3 bp):   
AGA

Found at i:14534 original size:18 final size:17

Alignment explanation


    Indices: 14511--14567  Score: 78
    Period size: 18  Copynumber: 3.2  Consensus size: 17

      14501 GTATTAAAGC

                              
      14511 AGAAGAAGAAGAAAGAAA
          1 AGAAGAAGAA-AAAGAAA

                            *
      14529 AGAAGAAGAAAAAGAAG
          1 AGAAGAAGAAAAAGAAA

                               
      14546 AGAAGGAAGAAAAAGAAGA
          1 AGAA-GAAGAAAAAGAA-A

               
      14565 AGA
          1 AGA

      14568 CGTTGCCCCG


Statistics
Matches: 35,  Mismatches: 2, Indels: 3
        0.88            0.05        0.08

Matches are distributed among these distances:
  17   10  0.29
  18   22  0.63
  19    3  0.09

ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00


Consensus pattern (17 bp):   
AGAAGAAGAAAAAGAAA

Found at i:14535 original size:21 final size:22

Alignment explanation


    Indices: 14506--14567  Score: 74
    Period size: 21  Copynumber: 2.9  Consensus size: 22

      14496 TGTGGGTATT

                *                 
      14506 AAAGCAGAAGAAGAAGAA-AGA
          1 AAAGAAGAAGAAGAAGAAGAGA

                        *         
      14527 AAAGAAGAAGAAAAAGAAGAG-
          1 AAAGAAGAAGAAGAAGAAGAGA

              *      *          
      14548 AAGGAAGAAAAAGAAGAAGA
          1 AAAGAAGAAGAAGAAGAAGA

      14568 CGTTGCCCCG


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  21   33  0.94
  22    2  0.06

ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00


Consensus pattern (22 bp):   
AAAGAAGAAGAAGAAGAAGAGA

Found at i:23908 original size:23 final size:22

Alignment explanation


    Indices: 23872--23915  Score: 61
    Period size: 23  Copynumber: 2.0  Consensus size: 22

      23862 AAAATATTTC

                     *             
      23872 ATTAAATAATTTGGGTTGAATTA
          1 ATTAAATAAATTGGGTT-AATTA

                 *               
      23895 ATTAATTAAATTGGGTTAATT
          1 ATTAAATAAATTGGGTTAATT

      23916 TTATTTCTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  22    4  0.21
  23   15  0.79

ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45


Consensus pattern (22 bp):   
ATTAAATAAATTGGGTTAATTA
Done.