Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000480.1 Kokia drynarioides strain JFW-HI SEQ_111355, 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: 8615
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39


Found at i:4289 original size:24 final size:24

Alignment explanation


    Indices: 4235--4293  Score: 75
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       4225 ATAATTTTTG

                                    
       4235 AGTTAAACTCTGTCTATTTGTTTC
          1 AGTTAAACTCTGTCTATTTGTTTC

             **          *          
       4259 AAATAAACTCTGTTTATTTG-TTC
          1 AGTTAAACTCTGTCTATTTGTTTC

                        
       4282 TAGTTAAACTCT
          1 -AGTTAAACTCT

       4294 TATTAGTCTA


Statistics
Matches: 29,  Mismatches: 5, Indels: 2
        0.81            0.14        0.06

Matches are distributed among these distances:
  23    3  0.10
  24   26  0.90

ACGTcount: A:0.27, C:0.15, G:0.10, T:0.47


Consensus pattern (24 bp):   
AGTTAAACTCTGTCTATTTGTTTC

Found at i:5476 original size:22 final size:21

Alignment explanation


    Indices: 5434--5474  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5424 AATAACATAA

                                 
       5434 ATTTCATAAAAATAAAAAAAT
          1 ATTTCATAAAAATAAAAAAAT

                       **       
       5455 ATTTCATAAAAGGAAAAAAA
          1 ATTTCATAAAAATAAAAAAA

       5475 ATCAAAAGAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24


Consensus pattern (21 bp):   
ATTTCATAAAAATAAAAAAAT

Found at i:5697 original size:15 final size:16

Alignment explanation


    Indices: 5677--5707  Score: 55
    Period size: 15  Copynumber: 2.0  Consensus size: 16

       5667 TTTTTTAGGG

                            
       5677 ATTTTTAAT-TTTTTT
          1 ATTTTTAATATTTTTT

                            
       5692 ATTTTTAATATTTTTT
          1 ATTTTTAATATTTTTT

       5708 TTAATTTTTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    9  0.60
  16    6  0.40

ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77


Consensus pattern (16 bp):   
ATTTTTAATATTTTTT

Found at i:6124 original size:23 final size:23

Alignment explanation


    Indices: 6086--6141  Score: 73
    Period size: 23  Copynumber: 2.6  Consensus size: 23

       6076 ACTTTTTGTC

                         *         
       6086 TATTAT-T-TATTTATTTATATG
          1 TATTATATATATTAATTTATATG

                              *    
       6107 TATTATATATATTAATTTTTATG
          1 TATTATATATATTAATTTATATG

                         
       6130 TATT-TATATATT
          1 TATTATATATATT

       6142 TTTAAATTTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  21    6  0.19
  22    9  0.29
  23   16  0.52

ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64


Consensus pattern (23 bp):   
TATTATATATATTAATTTATATG

Found at i:6149 original size:26 final size:26

Alignment explanation


    Indices: 6098--6170  Score: 73
    Period size: 26  Copynumber: 3.0  Consensus size: 26

       6088 TTATTTATTT

                *                *    
       6098 ATTTATATGTA-TTATATA-TATT-A
          1 ATTTTTATGTATTTATATATTTTTAA

                                      
       6121 ATTTTTATGTATTTATATATTTTTAA
          1 ATTTTTATGTATTTATATATTTTTAA

                   ***               
       6147 ATTTTTAAAAATTTATA-ATTTTTA
          1 ATTTTTATGTATTTATATATTTTTA

       6171 TATAAAAACA


Statistics
Matches: 42,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  23   10  0.24
  24    7  0.17
  25   10  0.24
  26   15  0.36

ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60


Consensus pattern (26 bp):   
ATTTTTATGTATTTATATATTTTTAA

Found at i:7117 original size:53 final size:53

Alignment explanation


    Indices: 7006--7116  Score: 129
    Period size: 53  Copynumber: 2.1  Consensus size: 53

       6996 TATTTATGTT

                              *                     *       *   *
       7006 ATTTTTCAATCAGTTTGATTTTTTATTTTGTATAACACTTTGTTATTTGAATT
          1 ATTTTTCAATCAGTTTGACTTTTTATTTTGTATAACACTTCGTTATTTCAATA

                   *   *                                           
       7059 ATTTTTCTATCGGTTTGACTTTTTATTTTGTAT-A-AC-TCGTTATTTCAATCCA
          1 ATTTTTCAATCAGTTTGACTTTTTATTTTGTATAACACTTCGTTATTTCAAT--A

                  
       7111 ATTTTT
          1 ATTTTT

       7117 TATTAAAAAA


Statistics
Matches: 50,  Mismatches: 6, Indels: 5
        0.82            0.10        0.08

Matches are distributed among these distances:
  50   11  0.22
  51    2  0.04
  52    7  0.14
  53   30  0.60

ACGTcount: A:0.23, C:0.11, G:0.09, T:0.58


Consensus pattern (53 bp):   
ATTTTTCAATCAGTTTGACTTTTTATTTTGTATAACACTTCGTTATTTCAATA

Found at i:8582 original size:20 final size:20

Alignment explanation


    Indices: 8557--8601  Score: 81
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       8547 AATGTGTTTC

                                
       8557 GTCCTCTAATGACTTCTCAT
          1 GTCCTCTAATGACTTCTCAT

                                
       8577 GTCCTCTAATGACTTCTCAT
          1 GTCCTCTAATGACTTCTCAT

            *    
       8597 TTCCT
          1 GTCCT

       8602 TGGTATTAGC


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  20   24  1.00

ACGTcount: A:0.18, C:0.31, G:0.09, T:0.42


Consensus pattern (20 bp):   
GTCCTCTAATGACTTCTCAT
Done.