Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010205.1 Kokia drynarioides strain JFW-HI SEQ_125023, 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, 943

Length: 1572
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33


Found at i:636 original size:12 final size:12

Alignment explanation


    Indices: 619--643  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        609 CAATATGTGT

                        
        619 AACTGGATTTTC
          1 AACTGGATTTTC

                        
        631 AACTGGATTTTC
          1 AACTGGATTTTC

             
        643 A
          1 A

        644 TCGCCATTCG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40


Consensus pattern (12 bp):   
AACTGGATTTTC

Found at i:1342 original size:4 final size:4

Alignment explanation


    Indices: 1322--1407  Score: 77
    Period size: 4  Copynumber: 21.2  Consensus size: 4

       1312 AACACATTAC

                       *                     *   *                     * 
       1322 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT C-TT CTTT CTTT CCTCT
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT -CTTT

             *      *                                      
       1370 CCTT CTTC CTTT CTTT CTTT CTTT CCTTT CTTT CTTT C
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT C

       1408 CCGTTTATTT


Statistics
Matches: 67,  Mismatches: 10, Indels: 10
        0.77            0.11        0.11

Matches are distributed among these distances:
   3    6  0.09
   4   51  0.76
   5   10  0.15

ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64


Consensus pattern (4 bp):   
CTTT

Found at i:1354 original size:20 final size:20

Alignment explanation


    Indices: 1329--1408  Score: 108
    Period size: 20  Copynumber: 3.9  Consensus size: 20

       1319 TACCTTTCTT

                                
       1329 TCCTTCTTCTTTCTTTCCTC
          1 TCCTTCTTCTTTCTTTCCTC

                                
       1349 TCCTTCTTCTTTCTTTCCTC
          1 TCCTTCTTCTTTCTTTCCTC

                                *
       1369 TCCTTCTTCCTTTCTTT-CTT
          1 TCCTTCTT-CTTTCTTTCCTC

              *                 
       1389 TCTTTCCTTTCTTTCTTTCC
          1 TCCTT-C-TTCTTTCTTTCC

       1409 CGTTTATTTG


Statistics
Matches: 54,  Mismatches: 2, Indels: 6
        0.87            0.03        0.10

Matches are distributed among these distances:
  20   34  0.63
  21   17  0.31
  22    3  0.06

ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62


Consensus pattern (20 bp):   
TCCTTCTTCTTTCTTTCCTC

Found at i:1356 original size:17 final size:17

Alignment explanation


    Indices: 1322--1407  Score: 92
    Period size: 17  Copynumber: 5.3  Consensus size: 17

       1312 AACACATTAC

                             
       1322 CTTTCTTTCC-TT-CTT
          1 CTTTCTTTCCTTTCCTT

                       *     
       1337 CTTTCTTTCCTCTCCTT
          1 CTTTCTTTCCTTTCCTT

                              
       1354 C-TTCTTT-CTTTCCTCT
          1 CTTTCTTTCCTTTCCT-T

             *            *  
       1370 CCTTC-TTCCTTTCTTT
          1 CTTTCTTTCCTTTCCTT

                          *  
       1386 CTTTCTTTCCTTTCTTT
          1 CTTTCTTTCCTTTCCTT

                 
       1403 CTTTC
          1 CTTTC

       1408 CCGTTTATTT


Statistics
Matches: 61,  Mismatches: 4, Indels: 10
        0.81            0.05        0.13

Matches are distributed among these distances:
  15   16  0.26
  16   16  0.26
  17   29  0.48

ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64


Consensus pattern (17 bp):   
CTTTCTTTCCTTTCCTT
Done.