Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004233.1 Kokia drynarioides strain JFW-HI SEQ_117495, 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: 8728
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34


Found at i:2179 original size:21 final size:21

Alignment explanation


    Indices: 2155--2196  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2145 TTTTTTCTTT

                   *             
       2155 AATTAATTAATCAAATATTAA
          1 AATTAATAAATCAAATATTAA

                 *          *    
       2176 AATTACTAAATCAAATTTTAA
          1 AATTAATAAATCAAATATTAA

       2197 TATTTCACCA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38


Consensus pattern (21 bp):   
AATTAATAAATCAAATATTAA

Found at i:5510 original size:30 final size:30

Alignment explanation


    Indices: 5452--5510  Score: 100
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       5442 TATTTTATTG

                                  **      
       5452 TTAATTTTGTTATTATTTTAGAGGCATTTA
          1 TTAATTTTGTTATTATTTTAGAAACATTTA

                                         
       5482 TTAATTTTGTTATTATTTTAGAAACATTT
          1 TTAATTTTGTTATTATTTTAGAAACATTT

       5511 GTTTGTTAAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58


Consensus pattern (30 bp):   
TTAATTTTGTTATTATTTTAGAAACATTTA

Found at i:5891 original size:26 final size:26

Alignment explanation


    Indices: 5837--5891  Score: 67
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       5827 ATGATTTTTT

                    *  *            * 
       5837 TGAAGATTTCAGTCTACAATTATTTG
          1 TGAAGATTGCAATCTACAATTATTGG

                                       
       5863 TGAAGATTGCAATCTACAATT-TTAGG
          1 TGAAGATTGCAATCTACAATTATT-GG

               
       5889 TGA
          1 TGA

       5892 CAATCTTAGA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  25    2  0.08
  26   23  0.92

ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38


Consensus pattern (26 bp):   
TGAAGATTGCAATCTACAATTATTGG

Found at i:7433 original size:19 final size:19

Alignment explanation


    Indices: 7395--7434  Score: 55
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       7385 AATCATTTTA

                         *     
       7395 AATATAATTATTTTTAGTG
          1 AATATAATTATTTATAGTG

                                
       7414 AATATAATT-TTTATATGTG
          1 AATATAATTATTTATA-GTG

              
       7433 AA
          1 AA

       7435 ATATTTCAAT


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

Matches are distributed among these distances:
  18    5  0.26
  19   14  0.74

ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50


Consensus pattern (19 bp):   
AATATAATTATTTATAGTG

Found at i:8054 original size:24 final size:24

Alignment explanation


    Indices: 8022--8081  Score: 120
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       8012 GTGTTTTGTA

                                    
       8022 GAAAGCGTTTTCAGGAAGCGCGTG
          1 GAAAGCGTTTTCAGGAAGCGCGTG

                                    
       8046 GAAAGCGTTTTCAGGAAGCGCGTG
          1 GAAAGCGTTTTCAGGAAGCGCGTG

                        
       8070 GAAAGCGTTTTC
          1 GAAAGCGTTTTC

       8082 TGACAAAACC


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   36  1.00

ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23


Consensus pattern (24 bp):   
GAAAGCGTTTTCAGGAAGCGCGTG
Done.