Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014117.1 Kokia drynarioides strain JFW-HI SEQ_129150, 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: 5995
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35


Found at i:3942 original size:29 final size:29

Alignment explanation


    Indices: 3904--3975  Score: 101
    Period size: 31  Copynumber: 2.4  Consensus size: 29

       3894 CATTTAACAC

                                  *       
       3904 AACAGTCACTCAACTTT-GAAATGTGACAA
          1 AACAGTCACT-AACTTTAGAAAAGTGACAA

                                           
       3933 AACAGTCACTAACTTTAGCGAAAAGTGACAA
          1 AACAGTCACTAACTTTA--GAAAAGTGACAA

                        
       3964 AACAGTCACTAA
          1 AACAGTCACTAA

       3976 AATCAGATGG


Statistics
Matches: 39,  Mismatches: 1, Indels: 4
        0.89            0.02        0.09

Matches are distributed among these distances:
  28    6  0.15
  29   10  0.26
  31   23  0.59

ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21


Consensus pattern (29 bp):   
AACAGTCACTAACTTTAGAAAAGTGACAA

Found at i:4468 original size:14 final size:14

Alignment explanation


    Indices: 4449--4478  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       4439 TTTGTTATTC

                          
       4449 ACATATTTTGGTTA
          1 ACATATTTTGGTTA

                     *    
       4463 ACATATTTTTGTTA
          1 ACATATTTTGGTTA

              
       4477 AC
          1 AC

       4479 GTCATTGTTC


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

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50


Consensus pattern (14 bp):   
ACATATTTTGGTTA

Found at i:4767 original size:50 final size:51

Alignment explanation


    Indices: 4693--4799  Score: 180
    Period size: 50  Copynumber: 2.1  Consensus size: 51

       4683 CGTAAAAAAA

                         *                    *                
       4693 TGACTGAAATGTATACCAAGTGACTATTTGTTTCTCCTTATCAAAATTGAG
          1 TGACTGAAATGTAAACCAAGTGACTATTTGTTTCCCCTTATCAAAATTGAG

                           *                                   
       4744 TGACTGAAA-GTAAATCAAGTGACTATTTGTTTCCCCTTATCAAAATTGAG
          1 TGACTGAAATGTAAACCAAGTGACTATTTGTTTCCCCTTATCAAAATTGAG

                  
       4794 TGACTG
          1 TGACTG

       4800 TTGTACAATT


Statistics
Matches: 53,  Mismatches: 3, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  50   44  0.83
  51    9  0.17

ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36


Consensus pattern (51 bp):   
TGACTGAAATGTAAACCAAGTGACTATTTGTTTCCCCTTATCAAAATTGAG

Found at i:4902 original size:15 final size:15

Alignment explanation


    Indices: 4860--4904  Score: 56
    Period size: 15  Copynumber: 3.0  Consensus size: 15

       4850 TCCACAGTAT

                           
       4860 AATTACATGATATAA
          1 AATTACATGATATAA

                *    *      
       4875 ATATGA-ATAATATAA
          1 A-ATTACATGATATAA

                           
       4890 AATTACATGATATAA
          1 AATTACATGATATAA

       4905 TAGAAAAAAT


Statistics
Matches: 24,  Mismatches: 4, Indels: 4
        0.75            0.12        0.12

Matches are distributed among these distances:
  14    3  0.12
  15   18  0.75
  16    3  0.12

ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33


Consensus pattern (15 bp):   
AATTACATGATATAA
Done.