Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001845.1 Kokia drynarioides strain JFW-HI SEQ_113598, 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: 2968
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39


Found at i:521 original size:29 final size:29

Alignment explanation


    Indices: 458--654  Score: 227
    Period size: 30  Copynumber: 6.7  Consensus size: 29

        448 TTGAACTATT

                                  *       
        458 CAAAAATTCCATTTTTACCCCTTAAACTTC
          1 CAAAAATTCCATTTTTACCCC-AAAACTTC

             *                            
        488 CCAAAATTCCATTTTTGACCCCAAAACTTC
          1 CAAAAATTCCATTTTT-ACCCCAAAACTTC

                                   *      
        518 CAAAAATTCCATTTTTACCCTC-GAACTTC
          1 CAAAAATTCCATTTTTACCC-CAAAACTTC

                   *            *     *   
        547 CAAAAATCCCATTTTTGACCTCAAAATTTC
          1 CAAAAATTCCATTTTT-ACCCCAAAACTTC

                                          
        577 CAAAAATTCCA-TTTTACCCCAAAAACTTC
          1 CAAAAATTCCATTTTTACCCC-AAAACTTC

                   *          *   *       
        606 CAAAAATGCCATTTTTAATCCCGAAACTTC
          1 CAAAAATTCCATTTTT-ACCCCAAAACTTC

            *         *        
        636 TAAAAATTCCGTTTTTACC
          1 CAAAAATTCCATTTTTACC

        655 GTCGAACCTC


Statistics
Matches: 142,  Mismatches: 18, Indels: 15
        0.81            0.10        0.09

Matches are distributed among these distances:
  28    4  0.03
  29   49  0.35
  30   80  0.56
  31    9  0.06

ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33


Consensus pattern (29 bp):   
CAAAAATTCCATTTTTACCCCAAAACTTC

Found at i:562 original size:59 final size:59

Alignment explanation


    Indices: 458--669  Score: 248
    Period size: 59  Copynumber: 3.6  Consensus size: 59

        448 TTGAACTATT

                                  *        *     *                      
        458 CAAAAATTCCATTTTTACCCCTTAAACTTCCCAAAATTCCATTTTTGACCCCAAAACTTC
          1 CAAAAATTCCATTTTTA-CCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTC

                                  *                          *     *   
        518 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCAAAATTTC
          1 CAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTC

                                                  *        * *   *       
        577 CAAAAATTCCA-TTTTACCC-CAAAAACTTCCAAAAATGCCATTTTTAATCCCGAAACTTC
          1 CAAAAATTCCATTTTTACCCTC--AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTC

            *         *        *  *   *       
        636 TAAAAATTCCGTTTTTACCGTCGAACCTCCAAAA
          1 CAAAAATTCCATTTTTACCCTCAAACTTCCAAAA

        670 TCTCTATTTT


Statistics
Matches: 130,  Mismatches: 18, Indels: 9
        0.83            0.11        0.06

Matches are distributed among these distances:
  57    1  0.01
  58    8  0.06
  59   96  0.74
  60   24  0.18
  61    1  0.01

ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32


Consensus pattern (59 bp):   
CAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTC

Found at i:710 original size:118 final size:118

Alignment explanation


    Indices: 458--714  Score: 313
    Period size: 118  Copynumber: 2.2  Consensus size: 118

        448 TTGAACTATT

                                 **        *     *        *                  
        458 CAAAAATTCCATTTTTACCCCTTAAACTTCCCAAAATTCCATTTTTGACCCCAAAACTTCCAAAA
          1 CAAAAATTCCA-TTTTACCCCAAAAACTTCCAAAAATGCCATTTTTAACCCCAAAACTTCCAAAA

                                 *                             *  
        523 ATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCAAAATTTC
         65 ATTCCATTTTTACCCTCGAACCTCCAAAAATCCCATTTTTGACCTCAAAATCTC

                                                           *   *       *     
        577 CAAAAATTCCATTTTACCCCAAAAACTTCCAAAAATGCCATTTTTAATCCCGAAACTTCTAAAAA
          1 CAAAAATTCCATTTTACCCCAAAAACTTCCAAAAATGCCATTTTTAACCCCAAAACTTCCAAAAA

                *        *                   *                     
        642 TTCCGTTTTTACCGTCGAACCTCC-AAAATCTCTATTTTCT-ACCTCAAAA-CTC
         66 TTCCATTTTTACCCTCGAACCTCCAAAAATC-CCATTTT-TGACCTCAAAATCTC

            **         *         
        694 TTAAAATTACCCTTTTACCCC
          1 CAAAAATT-CCATTTTACCCC

        715 CGAATGTCTA


Statistics
Matches: 119,  Mismatches: 16, Indels: 7
        0.84            0.11        0.05

Matches are distributed among these distances:
 117   14  0.12
 118   93  0.78
 119   12  0.10

ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33


Consensus pattern (118 bp):   
CAAAAATTCCATTTTACCCCAAAAACTTCCAAAAATGCCATTTTTAACCCCAAAACTTCCAAAAA
TTCCATTTTTACCCTCGAACCTCCAAAAATCCCATTTTTGACCTCAAAATCTC
Done.