Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008125.1 Kokia drynarioides strain JFW-HI SEQ_122783, 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: 8044
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32


Found at i:417 original size:23 final size:22

Alignment explanation


    Indices: 391--516  Score: 135
    Period size: 23  Copynumber: 5.5  Consensus size: 22

        381 ACATTAGCAC

                       * *         
        391 GCTTACTGTTCAGGACTGTGTGT
          1 GCTTACTGTT-TGCACTGTGTGT

                       *     * *   
        414 GCTTACTGATTCGCACTATATGT
          1 GCTTACTG-TTTGCACTGTGTGT

                                   
        437 GCTTACTGATTTGCACTGTGTGT
          1 GCTTACTG-TTTGCACTGTGTGT

                                   
        460 GCTTACTGTTTTGCACTGTGTGT
          1 GCTTACTG-TTTGCACTGTGTGT

              *     *              
        483 GCCTACTAATTTGCACTGTGTGT
          1 GCTTACT-GTTTGCACTGTGTGT

            *          
        506 ACTTACTGTTT
          1 GCTTACTGTTT

        517 CCTCAGCACT


Statistics
Matches: 88,  Mismatches: 13, Indels: 5
        0.83            0.12        0.05

Matches are distributed among these distances:
  22    3  0.03
  23   83  0.94
  24    2  0.02

ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43


Consensus pattern (22 bp):   
GCTTACTGTTTGCACTGTGTGT

Found at i:514 original size:46 final size:46

Alignment explanation


    Indices: 405--517  Score: 163
    Period size: 46  Copynumber: 2.5  Consensus size: 46

        395 ACTGTTCAGG

                             *                *    *      
        405 ACTGTGTGTGCTTACTGATTCGCACTATATGTGCTTACTGATTTGC
          1 ACTGTGTGTGCTTACTGTTTCGCACTATATGTGCCTACTAATTTGC

                                *     * *                 
        451 ACTGTGTGTGCTTACTGTTTTGCACTGTGTGTGCCTACTAATTTGC
          1 ACTGTGTGTGCTTACTGTTTCGCACTATATGTGCCTACTAATTTGC

                     *           
        497 ACTGTGTGTACTTACTGTTTC
          1 ACTGTGTGTGCTTACTGTTTC

        518 CTCAGCACTT


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

Matches are distributed among these distances:
  46   59  1.00

ACGTcount: A:0.15, C:0.19, G:0.22, T:0.43


Consensus pattern (46 bp):   
ACTGTGTGTGCTTACTGTTTCGCACTATATGTGCCTACTAATTTGC

Found at i:7702 original size:23 final size:23

Alignment explanation


    Indices: 7676--7784  Score: 125
    Period size: 23  Copynumber: 4.8  Consensus size: 23

       7666 TTACTGTTCA

                       *          *
       7676 GCACTGTGTGTTCTTACTGATTC
          1 GCACTGTGTGTGCTTACTGATTT

                 * *               
       7699 GCACTATATGTGCTTACTGATTT
          1 GCACTGTGTGTGCTTACTGATTT

                                    
       7722 GCAC--TGTGTGCTTACT-ATTTT
          1 GCACTGTGTGTGCTTACTGA-TTT

                         *    *    
       7743 GCACTGTGTGTGCCTACTAATTT
          1 GCACTGTGTGTGCTTACTGATTT

                       *       
       7766 GCACTGTGTGTACTTACTG
          1 GCACTGTGTGTGCTTACTG

       7785 TTTCCTCAGC


Statistics
Matches: 73,  Mismatches: 9, Indels: 8
        0.81            0.10        0.09

Matches are distributed among these distances:
  20    1  0.01
  21   18  0.25
  23   53  0.73
  24    1  0.01

ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42


Consensus pattern (23 bp):   
GCACTGTGTGTGCTTACTGATTT

Found at i:7747 original size:44 final size:45

Alignment explanation


    Indices: 7676--7784  Score: 132
    Period size: 44  Copynumber: 2.4  Consensus size: 45

       7666 TTACTGTTCA

                                                *    *    
       7676 GCACTGTGTGTTCTTACTGATTCGCACTATATGTGCTTACTGATTT
          1 GCACTGTGTG-TCTTACTGATTCGCACTATATGTGCCTACTAATTT

                                  *     * *               
       7722 GCACTGTGTG-CTTACT-ATTTTGCACTGTGTGTGCCTACTAATTT
          1 GCACTGTGTGTCTTACTGA-TTCGCACTATATGTGCCTACTAATTT

                               
       7766 GCACTGTGTGTACTTACTG
          1 GCACTGTGTGT-CTTACTG

       7785 TTTCCTCAGC


Statistics
Matches: 54,  Mismatches: 5, Indels: 7
        0.82            0.08        0.11

Matches are distributed among these distances:
  43    1  0.02
  44   37  0.69
  46   16  0.30

ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42


Consensus pattern (45 bp):   
GCACTGTGTGTCTTACTGATTCGCACTATATGTGCCTACTAATTT
Done.