Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006725.1 Kokia drynarioides strain JFW-HI SEQ_121321, 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: 7910
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:25 original size:17 final size:16

Alignment explanation


    Indices: 3--44  Score: 66
    Period size: 17  Copynumber: 2.6  Consensus size: 16

          1 TC

                            
          3 AAATAAATTTAAATTT
          1 AAATAAATTTAAATTT

                    *        
         19 AAAATAAACTTAAATTT
          1 -AAATAAATTTAAATTT

                     
         36 AAATAAATT
          1 AAATAAATT

         45 CAATTTCCAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  16    8  0.35
  17   15  0.65

ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38


Consensus pattern (16 bp):   
AAATAAATTTAAATTT

Found at i:914 original size:2 final size:2

Alignment explanation


    Indices: 907--936  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

        897 TCAAGGGTTA

                                             *          
        907 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        937 GCATATTGCT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:4200 original size:41 final size:41

Alignment explanation


    Indices: 4143--4230  Score: 176
    Period size: 41  Copynumber: 2.1  Consensus size: 41

       4133 TTGTATTAAA

                                                     
       4143 TATTTTCCTTTTCTATTGATATTAAGATTTAAATTTTATGT
          1 TATTTTCCTTTTCTATTGATATTAAGATTTAAATTTTATGT

                                                     
       4184 TATTTTCCTTTTCTATTGATATTAAGATTTAAATTTTATGT
          1 TATTTTCCTTTTCTATTGATATTAAGATTTAAATTTTATGT

                  
       4225 TATTTT
          1 TATTTT

       4231 ATTTATATTC


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  41   47  1.00

ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60


Consensus pattern (41 bp):   
TATTTTCCTTTTCTATTGATATTAAGATTTAAATTTTATGT

Found at i:5464 original size:3 final size:3

Alignment explanation


    Indices: 5456--5486  Score: 53
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       5446 TCATTAAGCC

                                                    
       5456 TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA

       5487 GGTATTGCAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   3   24  0.89
   4    3  0.11

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (3 bp):   
TAA

Found at i:6574 original size:11 final size:11

Alignment explanation


    Indices: 6558--6597  Score: 55
    Period size: 11  Copynumber: 3.7  Consensus size: 11

       6548 AATTTTTCAC

                       
       6558 TGTTGTTTTGT
          1 TGTTGTTTTGT

                      *
       6569 TGTTG-TTTGC
          1 TGTTGTTTTGT

             *         
       6579 TATTGTTTTGT
          1 TGTTGTTTTGT

                    
       6590 TGTTGTTT
          1 TGTTGTTT

       6598 ATTGCCATTT


Statistics
Matches: 24,  Mismatches: 4, Indels: 2
        0.80            0.13        0.07

Matches are distributed among these distances:
  10    8  0.33
  11   16  0.67

ACGTcount: A:0.03, C:0.03, G:0.25, T:0.70


Consensus pattern (11 bp):   
TGTTGTTTTGT

Found at i:7472 original size:17 final size:17

Alignment explanation


    Indices: 7448--7504  Score: 69
    Period size: 17  Copynumber: 3.4  Consensus size: 17

       7438 TTGGAAATTG

                             
       7448 AATTTATTTTAAATTTA
          1 AATTTATTTTAAATTTA

             *       *       
       7465 AGTTTATTTGAAATTTA
          1 AATTTATTTTAAATTTA

                    *    **  
       7482 AATTTATTATAAAACTA
          1 AATTTATTTTAAATTTA

                  
       7499 AATTTA
          1 AATTTA

       7505 GAAAAGTCCA


Statistics
Matches: 33,  Mismatches: 7, Indels: 0
        0.82            0.17        0.00

Matches are distributed among these distances:
  17   33  1.00

ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51


Consensus pattern (17 bp):   
AATTTATTTTAAATTTA
Done.