Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007471.1 Kokia drynarioides strain JFW-HI SEQ_122093, 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: 13478
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36


Found at i:1020 original size:26 final size:26

Alignment explanation


    Indices: 965--1028  Score: 69
    Period size: 26  Copynumber: 2.4  Consensus size: 26

        955 AATTGATTGC

                              *        
        965 AAAAAATAAAAATATTAACTTATGTAA
          1 AAAAAAT-AAAATATTAAATTATGTAA

                                        
        992 AAAAAATAAAATGATTAAAATT-TGT-A
          1 AAAAAATAAAAT-ATT-AAATTATGTAA

               *       
       1018 AAAGAATAAAA
          1 AAAAAATAAAA

       1029 AACATTTATT


Statistics
Matches: 33,  Mismatches: 2, Indels: 5
        0.82            0.05        0.12

Matches are distributed among these distances:
  26   16  0.48
  27   13  0.39
  28    4  0.12

ACGTcount: A:0.66, C:0.02, G:0.06, T:0.27


Consensus pattern (26 bp):   
AAAAAATAAAATATTAAATTATGTAA

Found at i:1029 original size:27 final size:25

Alignment explanation


    Indices: 965--1029  Score: 69
    Period size: 27  Copynumber: 2.5  Consensus size: 25

        955 AATTGATTGC

                              *      
        965 AAAAAATAAAAATATTAACTTATGT
          1 AAAAAATAAAAATATTAAATTATGT

                  *                     
        990 AAAAAAAATAAAATGATTAAAATT-TGT
          1 AAAAAATA-AAAAT-ATT-AAATTATGT

                         
       1017 AAAAGAATAAAAA
          1 AAAA-AATAAAAA

       1030 ACATTTATTT


Statistics
Matches: 33,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
  25    7  0.21
  26    5  0.15
  27   14  0.42
  28    7  0.21

ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26


Consensus pattern (25 bp):   
AAAAAATAAAAATATTAAATTATGT

Found at i:1211 original size:16 final size:16

Alignment explanation


    Indices: 1187--1242  Score: 69
    Period size: 16  Copynumber: 3.5  Consensus size: 16

       1177 TATTTTAAGT

                          * 
       1187 AATTTAATTAAAATCA
          1 AATTTAATTAAAATAA

                *           
       1203 AATTAAATTAAAA-AA
          1 AATTTAATTAAAATAA

                           * 
       1218 ATATTTAATTAAAATTA
          1 A-ATTTAATTAAAATAA

                    
       1235 AATTTAAT
          1 AATTTAAT

       1243 AATGTTACAC


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
  15    2  0.06
  16   30  0.88
  17    2  0.06

ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39


Consensus pattern (16 bp):   
AATTTAATTAAAATAA

Found at i:2679 original size:29 final size:29

Alignment explanation


    Indices: 2635--2692  Score: 80
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       2625 CGGTGTCGTA

                 *                 *     
       2635 CACTTGGTTGGCACTTGAAAAATGAGGGT
          1 CACTTCGTTGGCACTTGAAAAATAAGGGT

                       *        *        
       2664 CACTTCGTTGGTACTTGAAAGATAAGGGT
          1 CACTTCGTTGGCACTTGAAAAATAAGGGT

       2693 TAAAACCTTA


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29


Consensus pattern (29 bp):   
CACTTCGTTGGCACTTGAAAAATAAGGGT

Found at i:3933 original size:20 final size:20

Alignment explanation


    Indices: 3908--3949  Score: 84
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       3898 TTTCTAAGTT

                                
       3908 ATTTTAGTACCTGAGTGGTG
          1 ATTTTAGTACCTGAGTGGTG

                                
       3928 ATTTTAGTACCTGAGTGGTG
          1 ATTTTAGTACCTGAGTGGTG

              
       3948 AT
          1 AT

       3950 AATGAGAAGC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40


Consensus pattern (20 bp):   
ATTTTAGTACCTGAGTGGTG

Found at i:11829 original size:27 final size:27

Alignment explanation


    Indices: 11796--11850  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      11786 TATTAAACAC

                                       
      11796 TGTTAAATTCTCTCTCTTTATTATTAT
          1 TGTTAAATTCTCTCTCTTTATTATTAT

                                       
      11823 TGTTAAATTCTCTCTCTTTATTATTAT
          1 TGTTAAATTCTCTCTCTTTATTATTAT

             
      11850 T
          1 T

      11851 ATTTTTTCTA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.22, C:0.15, G:0.04, T:0.60


Consensus pattern (27 bp):   
TGTTAAATTCTCTCTCTTTATTATTAT
Done.