Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008045.1 Kokia drynarioides strain JFW-HI SEQ_122701, 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: 33439
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34


Found at i:4184 original size:24 final size:23

Alignment explanation


    Indices: 4135--4191  Score: 78
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       4125 TCGAACATGT

                 *     *           
       4135 AACATATTCATGAACATTAAACG
          1 AACATGTTCATAAACATTAAACG

                                  * 
       4158 AACATGTTCATAAACATATAAATG
          1 AACATGTTCATAAACAT-TAAACG

                      
       4182 AACATGTTCA
          1 AACATGTTCA

       4192 CGAACAATGT


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  23   15  0.50
  24   15  0.50

ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28


Consensus pattern (23 bp):   
AACATGTTCATAAACATTAAACG

Found at i:4197 original size:24 final size:23

Alignment explanation


    Indices: 4135--4197  Score: 81
    Period size: 24  Copynumber: 2.7  Consensus size: 23

       4125 TCGAACATGT

                 *                 
       4135 AACATATTCATGAACATTAAACG
          1 AACATGTTCATGAACATTAAACG

                       *          * 
       4158 AACATGTTCATAAACATATAAATG
          1 AACATGTTCATGAACAT-TAAACG

                      *     
       4182 AACATGTTCACGAACA
          1 AACATGTTCATGAACA

       4198 ATGTTAATGA


Statistics
Matches: 34,  Mismatches: 5, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  23   15  0.44
  24   19  0.56

ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25


Consensus pattern (23 bp):   
AACATGTTCATGAACATTAAACG

Found at i:9636 original size:17 final size:17

Alignment explanation


    Indices: 9614--9647  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       9604 AGCGAGTGCC

                  *  *       
       9614 TTGAATGTGTGAGCTCA
          1 TTGAATATGCGAGCTCA

                             
       9631 TTGAATATGCGAGCTCA
          1 TTGAATATGCGAGCTCA

       9648 CCTAAGTTAA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32


Consensus pattern (17 bp):   
TTGAATATGCGAGCTCA

Found at i:13982 original size:16 final size:15

Alignment explanation


    Indices: 13940--13983  Score: 52
    Period size: 16  Copynumber: 2.8  Consensus size: 15

      13930 TTTTATTTAA

                      *    
      13940 AAATTTTATATAATT
          1 AAATTTTATAAAATT

                 *          
      13955 AATATATTATAAAATT
          1 AA-ATTTTATAAAATT

                         
      13971 AAATTTTCATAAA
          1 AAATTTT-ATAAA

      13984 TATATATATA


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

Matches are distributed among these distances:
  15    6  0.25
  16   18  0.75

ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45


Consensus pattern (15 bp):   
AAATTTTATAAAATT

Found at i:26192 original size:22 final size:25

Alignment explanation


    Indices: 26145--26194  Score: 70
    Period size: 22  Copynumber: 2.1  Consensus size: 25

      26135 GTTTTCTTAT

                              *      
      26145 AAAAATAACTATGAAAATTTAAATA
          1 AAAAATAACTATGAAAATATAAATA

                                     
      26170 AAAAAT-AC-ATGAAAA-ATAAATA
          1 AAAAATAACTATGAAAATATAAATA

               
      26192 AAA
          1 AAA

      26195 TGCAATAAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  22    9  0.38
  23    7  0.29
  24    2  0.08
  25    6  0.25

ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22


Consensus pattern (25 bp):   
AAAAATAACTATGAAAATATAAATA

Found at i:27433 original size:6 final size:6

Alignment explanation


    Indices: 27422--27449  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

      27412 GAGTGGGCCA

                                            
      27422 TCAGGG TCAGGG TCAGGG TCAGGG TCAG
          1 TCAGGG TCAGGG TCAGGG TCAGGG TCAG

      27450 TGTGATTAAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.18, C:0.18, G:0.46, T:0.18


Consensus pattern (6 bp):   
TCAGGG

Done.