Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000959.1 Kokia drynarioides strain JFW-HI SEQ_112134, 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: 20369
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:2434 original size:21 final size:21

Alignment explanation


    Indices: 2410--2449  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2400 TAGAATCCAA

                *                
       2410 AGTTGTATCAATAGAACTCCG
          1 AGTTCTATCAATAGAACTCCG

                     *         
       2431 AGTTCTATCGATAGAACTC
          1 AGTTCTATCAATAGAACTC

       2450 TACAGATTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Consensus pattern (21 bp):   
AGTTCTATCAATAGAACTCCG

Found at i:4879 original size:7 final size:7

Alignment explanation


    Indices: 4867--4894  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

       4857 ATTTAAATAT

                   
       4867 TCAACAC
          1 TCAACAC

                   
       4874 TCAACAC
          1 TCAACAC

                   
       4881 TCAACAC
          1 TCAACAC

                   
       4888 TCAACAC
          1 TCAACAC

       4895 ATTTGATTTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14


Consensus pattern (7 bp):   
TCAACAC

Found at i:4946 original size:13 final size:14

Alignment explanation


    Indices: 4917--4946  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       4907 TTCAGTACAT

                          
       4917 TGACATTTAACCTC
          1 TGACATTTAACCTC

                          
       4931 TGACATTTAA-CTC
          1 TGACATTTAACCTC

               
       4944 TGA
          1 TGA

       4947 TTGCGTTGAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    6  0.38
  14   10  0.62

ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37


Consensus pattern (14 bp):   
TGACATTTAACCTC

Found at i:12784 original size:21 final size:21

Alignment explanation


    Indices: 12759--12805  Score: 60
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      12749 TGACCATCTA

                    *             
      12759 AAGGAAAAGGAAGAAGA-AGAG
          1 AAGGAAAAAG-AGAAGAGAGAG

                          *      
      12780 AAGGAAAAAGAGAATAGAGAG
          1 AAGGAAAAAGAGAAGAGAGAG

                 
      12801 AAGGA
          1 AAGGA

      12806 CCCTGCCAAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  20    5  0.22
  21   18  0.78

ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02


Consensus pattern (21 bp):   
AAGGAAAAAGAGAAGAGAGAG

Found at i:15447 original size:13 final size:14

Alignment explanation


    Indices: 15418--15447  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      15408 TTCAGTACAT

                          
      15418 TGACATTTAACCTC
          1 TGACATTTAACCTC

                          
      15432 TGACATTTAA-CTC
          1 TGACATTTAACCTC

               
      15445 TGA
          1 TGA

      15448 TTGCATTGAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    6  0.38
  14   10  0.62

ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37


Consensus pattern (14 bp):   
TGACATTTAACCTC
Done.