Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000875.1 Kokia drynarioides strain JFW-HI SEQ_111995, 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: 16550
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32


Found at i:1558 original size:6 final size:6

Alignment explanation


    Indices: 1547--1652  Score: 72
    Period size: 6  Copynumber: 17.5  Consensus size: 6

       1537 ACCCATTGTT

                                   *     *        **           *   *
       1547 TTTTTA TTTTTA -TTTTA TTATTA -ATTTA TTTCGA TTATTTA TATTTC
          1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA

             *             *                 *                 * *   
       1594 TATTTA TTTTTA TCTTTA TTTTTA TTTTAAA TTTTTA TTTATTA ATATTA
          1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT-TA TTTTTA TTT-TTA TTTTTA

                      
       1644 TTTTTA TTT
          1 TTTTTA TTT

       1653 CTTTTTCAGA


Statistics
Matches: 75,  Mismatches: 20, Indels: 10
        0.71            0.19        0.10

Matches are distributed among these distances:
   5    8  0.11
   6   55  0.73
   7   12  0.16

ACGTcount: A:0.25, C:0.03, G:0.01, T:0.72


Consensus pattern (6 bp):   
TTTTTA

Found at i:1627 original size:13 final size:11

Alignment explanation


    Indices: 1548--1633  Score: 75
    Period size: 11  Copynumber: 7.3  Consensus size: 11

       1538 CCCATTGTTT

                       
       1548 TTTTATTTTTA
          1 TTTTATTTTTA

                   *   
       1559 TTTTATTATTA
          1 TTTTATTTTTA

            *             
       1570 ATTTATTTCGATTA
          1 TTTTATTT---TTA

                     *  
       1584 TTTATATTTCTA
          1 TTT-TATTTTTA

                       
       1596 -TTTATTTTTA
          1 TTTTATTTTTA

                        
       1606 TCTTTATTTTTA
          1 T-TTTATTTTTA

                         
       1618 TTTTAAATTTTTA
          1 TTTT--ATTTTTA

               
       1631 TTT
          1 TTT

       1634 ATTAATATTA


Statistics
Matches: 61,  Mismatches: 6, Indels: 14
        0.75            0.07        0.17

Matches are distributed among these distances:
  10    7  0.11
  11   21  0.34
  12   13  0.21
  13   10  0.16
  14    5  0.08
  15    5  0.08

ACGTcount: A:0.23, C:0.03, G:0.01, T:0.72


Consensus pattern (11 bp):   
TTTTATTTTTA

Found at i:2547 original size:20 final size:20

Alignment explanation


    Indices: 2522--2559  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2512 AATTTCGAAT

                  *  *          
       2522 AAAGAAGAAGAAAAAAAAGA
          1 AAAGAACAACAAAAAAAAGA

                              
       2542 AAAGAACAACAAAAAAAA
          1 AAAGAACAACAAAAAAAA

       2560 TAGAAAACTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00


Consensus pattern (20 bp):   
AAAGAACAACAAAAAAAAGA

Found at i:3437 original size:23 final size:23

Alignment explanation


    Indices: 3382--3440  Score: 82
    Period size: 23  Copynumber: 2.6  Consensus size: 23

       3372 CTGGCATGGC

                                   
       3382 GTCTAGTCAGCAACTTCTAGAAG
          1 GTCTAGTCAGCAACTTCTAGAAG

            *  * *      *          
       3405 ATCCAATCAGCAGCTTCTAGAAG
          1 GTCTAGTCAGCAACTTCTAGAAG

                         
       3428 GTCTAGTCAGCAA
          1 GTCTAGTCAGCAA

       3441 GGATGGATGA


Statistics
Matches: 28,  Mismatches: 8, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  23   28  1.00

ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24


Consensus pattern (23 bp):   
GTCTAGTCAGCAACTTCTAGAAG
Done.