Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009851.1 Kokia drynarioides strain JFW-HI SEQ_124580, 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: 15280
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31

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


Found at i:2103 original size:14 final size:13

Alignment explanation


    Indices: 2077--2139  Score: 56
    Period size: 13  Copynumber: 4.8  Consensus size: 13

       2067 AATATTACGA

                         
       2077 ATAAATATTTCAT
          1 ATAAATATTTCAT

                          
       2090 ATAAATACTTTCAT
          1 ATAAATA-TTTCAT

                  *     * 
       2104 A-ATAACATTTCGT
          1 ATA-AATATTTCAT

            *   *        
       2117 GTAACTATTTCAT
          1 ATAAATATTTCAT

            *         
       2130 CTAAATATTT
          1 ATAAATATTT

       2140 TACTTTACTA


Statistics
Matches: 39,  Mismatches: 8, Indels: 6
        0.74            0.15        0.11

Matches are distributed among these distances:
  13   28  0.72
  14   11  0.28

ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44


Consensus pattern (13 bp):   
ATAAATATTTCAT

Found at i:5673 original size:71 final size:71

Alignment explanation


    Indices: 5575--5775  Score: 348
    Period size: 71  Copynumber: 2.8  Consensus size: 71

       5565 ATTAGAATGT

                   *              *                                          
       5575 CATAGCCTAGCTATGGTCTTACCTATATACACTGCCATGGTCCAACCATGGTCTTACGTTTGAAT
          1 CATAGCCCAGCTATGGTCTTACATATATACACTGCCATGGTCCAACCATGGTCTTACGTTTGAAT

                  
       5640 AACTGC
         66 AACTGC

                             *    *        *                                 
       5646 CATAGCCCAGCTATGGTATTACGTATATACATTGCCATGGTCCAACCATGGTCTTACGTTTGAAT
          1 CATAGCCCAGCTATGGTCTTACATATATACACTGCCATGGTCCAACCATGGTCTTACGTTTGAAT

                  
       5711 AACTGC
         66 AACTGC

                     *                                                 
       5717 CATAGCCCAACTATGGTCTTACATATATACACTGCCATGGTCCAACCATGGTCTTACGT
          1 CATAGCCCAGCTATGGTCTTACATATATACACTGCCATGGTCCAACCATGGTCTTACGT

       5776 CAGAATGCAG


Statistics
Matches: 122,  Mismatches: 8, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  71  122  1.00

ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30


Consensus pattern (71 bp):   
CATAGCCCAGCTATGGTCTTACATATATACACTGCCATGGTCCAACCATGGTCTTACGTTTGAAT
AACTGC

Found at i:5697 original size:35 final size:35

Alignment explanation


    Indices: 5587--5775  Score: 211
    Period size: 35  Copynumber: 5.3  Consensus size: 35

       5577 TAGCCTAGCT

                      *                        
       5587 ATGGTCTTACCTATATACACTGCCATGGTCCAACC
          1 ATGGTCTTACGTATATACACTGCCATGGTCCAACC

                        *               * *   * *
       5622 ATGGTCTTACGTTTGAATA-ACTGCCATAGCCCAGCT
          1 ATGGTCTTACGTAT--ATACACTGCCATGGTCCAACC

                 *             *               
       5658 ATGGTATTACGTATATACATTGCCATGGTCCAACC
          1 ATGGTCTTACGTATATACACTGCCATGGTCCAACC

                        *               * *     *
       5693 ATGGTCTTACGTTTGAATA-ACTGCCATAGCCCAACT
          1 ATGGTCTTACGTAT--ATACACTGCCATGGTCCAACC

                      *                        
       5729 ATGGTCTTACATATATACACTGCCATGGTCCAACC
          1 ATGGTCTTACGTATATACACTGCCATGGTCCAACC

                        
       5764 ATGGTCTTACGT
          1 ATGGTCTTACGT

       5776 CAGAATGCAG


Statistics
Matches: 123,  Mismatches: 25, Indels: 12
        0.77            0.16        0.08

Matches are distributed among these distances:
  34    6  0.05
  35   61  0.50
  36   50  0.41
  37    6  0.05

ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31


Consensus pattern (35 bp):   
ATGGTCTTACGTATATACACTGCCATGGTCCAACC

Found at i:5988 original size:21 final size:21

Alignment explanation


    Indices: 5964--6015  Score: 61
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       5954 TGAGACAATA

                                  
       5964 CTACCGATACAAGT-ATGACTT
          1 CTACCGATACAAGTCATG-CTT

                   *   *         
       5985 CTACCGAAACATGTCATGCTT
          1 CTACCGATACAAGTCATGCTT

                 *    
       6006 CTACCTATAC
          1 CTACCGATAC

       6016 TAAAAACTCC


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  21   23  0.88
  22    3  0.12

ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29


Consensus pattern (21 bp):   
CTACCGATACAAGTCATGCTT
Done.