Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007343.1 Kokia drynarioides strain JFW-HI SEQ_121959, 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: 11912
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:3892 original size:27 final size:28

Alignment explanation


    Indices: 3855--3938  Score: 84
    Period size: 27  Copynumber: 3.0  Consensus size: 28

       3845 TAATAGCAAA

                                 *      
       3855 ACAACAACAAAAACAAAAATATTAGC-A
          1 ACAACAACAAAAACAAAAATAATAGCAA

                                   *     
       3882 ACAA-AATCAAAAACAAAAATAACAGCAA
          1 ACAACAA-CAAAAACAAAAATAATAGCAA

                                  *       
       3910 A-AACAACACCAAAACAATAAAAAATAGCA
          1 ACAACAACA--AAAACAA-AAATAATAGCA

       3939 TCAAAACAAC


Statistics
Matches: 47,  Mismatches: 4, Indels: 9
        0.78            0.07        0.15

Matches are distributed among these distances:
  26    2  0.04
  27   25  0.53
  28    4  0.09
  29    7  0.15
  30    9  0.19

ACGTcount: A:0.69, C:0.19, G:0.04, T:0.08


Consensus pattern (28 bp):   
ACAACAACAAAAACAAAAATAATAGCAA

Found at i:3932 original size:21 final size:21

Alignment explanation


    Indices: 3908--3947  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       3898 AAATAACAGC

                                 
       3908 AAAAACAACACCAAAACAATA
          1 AAAAACAACACCAAAACAATA

                 * *  *        
       3929 AAAAATAGCATCAAAACAA
          1 AAAAACAACACCAAAACAA

       3948 CAATATGATT


Statistics
Matches: 16,  Mismatches: 3, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   16  1.00

ACGTcount: A:0.70, C:0.20, G:0.03, T:0.07


Consensus pattern (21 bp):   
AAAAACAACACCAAAACAATA

Found at i:4487 original size:26 final size:28

Alignment explanation


    Indices: 4434--4493  Score: 70
    Period size: 28  Copynumber: 2.2  Consensus size: 28

       4424 ATGAAGTGTA

                    *  *           *    
       4434 TTTTTTTATTTTTCACTTAAACATGTTT
          1 TTTTTTTAATTGTCACTTAAACAAGTTT

                                        
       4462 TTTTTTTAATTGT-ACTTAAA-AAGTTT
          1 TTTTTTTAATTGTCACTTAAACAAGTTT

             *    
       4488 TATTTT
          1 TTTTTT

       4494 ATACTCAATA


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  26   10  0.36
  27    7  0.25
  28   11  0.39

ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63


Consensus pattern (28 bp):   
TTTTTTTAATTGTCACTTAAACAAGTTT

Found at i:6592 original size:26 final size:26

Alignment explanation


    Indices: 6491--6583  Score: 132
    Period size: 26  Copynumber: 3.6  Consensus size: 26

       6481 ACATATTTCC

                       *   *  *       
       6491 TCAAAATTTTATTAGAGGCAAAATCG
          1 TCAAAATTTTACTAGGGGTAAAATCG

                  *                 * 
       6517 TCAAAACTTTACTAGGGGTAAAATTG
          1 TCAAAATTTTACTAGGGGTAAAATCG

                                      
       6543 TCAAAATTTTACTAGGGGTAAAATCG
          1 TCAAAATTTTACTAGGGGTAAAATCG

                      *    
       6569 TCAAAATTTTGCTAG
          1 TCAAAATTTTACTAG

       6584 AAATAAAATA


Statistics
Matches: 59,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  26   59  1.00

ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32


Consensus pattern (26 bp):   
TCAAAATTTTACTAGGGGTAAAATCG

Found at i:7901 original size:38 final size:38

Alignment explanation


    Indices: 7823--7901  Score: 113
    Period size: 38  Copynumber: 2.1  Consensus size: 38

       7813 CACATTCATT

                               *       *      **  
       7823 TATAGTTTCAACGAGTTAGGGGAGGGATCGATTGGTCA
          1 TATAGTTTCAACGAGTTAGCGGAGGGACCGATTGACCA

                                 *                
       7861 TATAGTTTCAACGAGTTAGCGTAGGGACCGATTGACCA
          1 TATAGTTTCAACGAGTTAGCGGAGGGACCGATTGACCA

               
       7899 TAT
          1 TAT

       7902 GTAGTTGAGG


Statistics
Matches: 36,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  38   36  1.00

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


Consensus pattern (38 bp):   
TATAGTTTCAACGAGTTAGCGGAGGGACCGATTGACCA
Done.