Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013054.1 Kokia drynarioides strain JFW-HI SEQ_128072, 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: 37790
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:9132 original size:20 final size:20

Alignment explanation


    Indices: 9107--9151  Score: 67
    Period size: 18  Copynumber: 2.4  Consensus size: 20

       9097 ACATATTTTA

                                
       9107 ATTTTAAAATTGTCAAATAT
          1 ATTTTAAAATTGTCAAATAT

                            *   
       9127 ATTTT--AATTGTCAAGTAT
          1 ATTTTAAAATTGTCAAATAT

                   
       9145 ATTTTAA
          1 ATTTTAA

       9152 TTTTTTAAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  18   17  0.77
  20    5  0.23

ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49


Consensus pattern (20 bp):   
ATTTTAAAATTGTCAAATAT

Found at i:9137 original size:18 final size:18

Alignment explanation


    Indices: 9114--9153  Score: 71
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       9104 TTAATTTTAA

                              
       9114 AATTGTCAAATATATTTT
          1 AATTGTCAAATATATTTT

                     *        
       9132 AATTGTCAAGTATATTTT
          1 AATTGTCAAATATATTTT

                
       9150 AATT
          1 AATT

       9154 TTTTAAAAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50


Consensus pattern (18 bp):   
AATTGTCAAATATATTTT

Found at i:15059 original size:7 final size:7

Alignment explanation


    Indices: 15044--15073  Score: 53
    Period size: 7  Copynumber: 4.4  Consensus size: 7

      15034 TGATTTCTGC

                   
      15044 AAAAA-A
          1 AAAAAGA

                   
      15050 AAAAAGA
          1 AAAAAGA

                   
      15057 AAAAAGA
          1 AAAAAGA

                   
      15064 AAAAAGA
          1 AAAAAGA

               
      15071 AAA
          1 AAA

      15074 GGTAATGAAC


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6    5  0.22
   7   18  0.78

ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00


Consensus pattern (7 bp):   
AAAAAGA

Found at i:32433 original size:15 final size:15

Alignment explanation


    Indices: 32408--32446  Score: 51
    Period size: 15  Copynumber: 2.6  Consensus size: 15

      32398 ATGATCATGA

                *        * 
      32408 CATCATCATCATCGT
          1 CATCTTCATCATCAT

             *             
      32423 CTTCTTCATCATCAT
          1 CATCTTCATCATCAT

                     
      32438 CATCTTCAT
          1 CATCTTCAT

      32447 ACTGGGTTTC


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.23, C:0.33, G:0.03, T:0.41


Consensus pattern (15 bp):   
CATCTTCATCATCAT

Found at i:32433 original size:18 final size:18

Alignment explanation


    Indices: 32410--32444  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      32400 GATCATGACA

                       *      
      32410 TCATCATCATCGTCTTCT
          1 TCATCATCATCATCTTCT

                             
      32428 TCATCATCATCATCTTC
          1 TCATCATCATCATCTTC

      32445 ATACTGGGTT


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

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.20, C:0.34, G:0.03, T:0.43


Consensus pattern (18 bp):   
TCATCATCATCATCTTCT
Done.