Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000840.1 Kokia drynarioides strain JFW-HI SEQ_111938, 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: 15400
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--39  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

                                                                      
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         40 TGAGAAAGAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:404 original size:26 final size:26

Alignment explanation


    Indices: 375--430  Score: 78
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        365 GAGCACATTC

                         *             
        375 CTTTCACT-TTACTCCACAAAGGCTTT
          1 CTTTCA-TATTACACCACAAAGGCTTT

                                  *   
        401 CTTTCATATTACACCACAAAGGTTTT
          1 CTTTCATATTACACCACAAAGGCTTT

                
        427 CTTT
          1 CTTT

        431 GTTGACGTGT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  25    1  0.04
  26   26  0.96

ACGTcount: A:0.25, C:0.27, G:0.07, T:0.41


Consensus pattern (26 bp):   
CTTTCATATTACACCACAAAGGCTTT

Found at i:2951 original size:24 final size:24

Alignment explanation


    Indices: 2924--2970  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2914 AAACTTCGGT

                     *              
       2924 TTAATGCAATTATATATATAAAAA
          1 TTAATGCAAATATATATATAAAAA

                 **                
       2948 TTAATTTAAATATATATATAAAA
          1 TTAATGCAAATATATATATAAAA

       2971 TAAATATATC


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

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40


Consensus pattern (24 bp):   
TTAATGCAAATATATATATAAAAA

Found at i:3030 original size:22 final size:25

Alignment explanation


    Indices: 2982--3029  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 25

       2972 AAATATATCA

                          *          
       2982 AATTATTTTTATATTAAATAAATAT
          1 AATTATTTTTATATGAAATAAATAT

                           *        
       3007 AATT-TTTTTATATGCAATAAATA
          1 AATTATTTTTATATGAAATAAATA

       3030 AATATTAAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  24   17  0.81
  25    4  0.19

ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50


Consensus pattern (25 bp):   
AATTATTTTTATATGAAATAAATAT
Done.