Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009309.1 Kokia drynarioides strain JFW-HI SEQ_124016, 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: 13458
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33


Found at i:3531 original size:41 final size:41

Alignment explanation


    Indices: 3486--3567  Score: 146
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       3476 AAAATTACTT

                                         *           
       3486 ATTTTAATTACGTAAGAACATTCTCATAAGCTTTTAATCAA
          1 ATTTTAATTACGTAAGAACATTCTCATAAACTTTTAATCAA

                      *                              
       3527 ATTTTAATTATGTAAGAACATTCTCATAAACTTTTAATCAA
          1 ATTTTAATTACGTAAGAACATTCTCATAAACTTTTAATCAA

       3568 TTTGATATTC


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  41   39  1.00

ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40


Consensus pattern (41 bp):   
ATTTTAATTACGTAAGAACATTCTCATAAACTTTTAATCAA

Found at i:6955 original size:36 final size:36

Alignment explanation


    Indices: 6901--7042  Score: 169
    Period size: 36  Copynumber: 3.9  Consensus size: 36

       6891 CTGTTATGAA

                  *                             
       6901 AGTAAACATGTGGGTATGTTATTCATGCCATGTGAC
          1 AGTAAATATGTGGGTATGTTATTCATGCCATGTGAC

                    *   **            *         *
       6937 AGTAAATACGTGAATATGTTATTCATACCA-GATGAT
          1 AGTAAATATGTGGGTATGTTATTCATGCCATG-TGAC

                                    *       *   
       6973 AGTAAATATGTGGGTATGTTATTCCTGCCATGAGAC
          1 AGTAAATATGTGGGTATGTTATTCATGCCATGTGAC

            *     *                   *       
       7009 CGTAAAAATGTGGGTATGTTATTCATTCCATGTG
          1 AGTAAATATGTGGGTATGTTATTCATGCCATGTG

       7043 GTAATGAATA


Statistics
Matches: 86,  Mismatches: 18, Indels: 4
        0.80            0.17        0.04

Matches are distributed among these distances:
  35    1  0.01
  36   84  0.98
  37    1  0.01

ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35


Consensus pattern (36 bp):   
AGTAAATATGTGGGTATGTTATTCATGCCATGTGAC

Found at i:7027 original size:72 final size:72

Alignment explanation


    Indices: 6896--7034  Score: 197
    Period size: 72  Copynumber: 1.9  Consensus size: 72

       6886 GATGACTGTT

                                                 *         *                 
       6896 ATGAAAGTAAACATGTGGGTATGTTATTCATGCCATGTGACAGTAAATACGTGAATATGTTATTC
          1 ATGAAAGTAAACATGTGGGTATGTTATTCATGCCATGAGACAGTAAAAACGTGAATATGTTATTC

                   
       6961 ATACCAG
         66 ATACCAG

                *      *                 *           *       *   **          
       6968 ATGATAGTAAATATGTGGGTATGTTATTCCTGCCATGAGACCGTAAAAATGTGGGTATGTTATTC
          1 ATGAAAGTAAACATGTGGGTATGTTATTCATGCCATGAGACAGTAAAAACGTGAATATGTTATTC

              
       7033 AT
         66 AT

       7035 TCCATGTGGT


Statistics
Matches: 58,  Mismatches: 9, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  72   58  1.00

ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34


Consensus pattern (72 bp):   
ATGAAAGTAAACATGTGGGTATGTTATTCATGCCATGAGACAGTAAAAACGTGAATATGTTATTC
ATACCAG

Found at i:7571 original size:58 final size:58

Alignment explanation


    Indices: 7464--7589  Score: 148
    Period size: 58  Copynumber: 2.2  Consensus size: 58

       7454 GTGATTATTA

                                                      * *             
       7464 GATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTTATGTGACTAATGT
          1 GATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATACTCATGTGACTAATGT

                                  *    *           **           *  *   
       7522 GATTAAATGTGATTAATATGTGTTGTGTTAAATGCTT-ATGTACTCATGTGATTATTGT
          1 GATTAAATGTGATTAATATGTGATGTGATAAATG-TTGAAATACTCATGTGACTAATGT

            *          
       7580 AATT-AATGTG
          1 GATTAAATGTG

       7590 TAAAAGAATG


Statistics
Matches: 58,  Mismatches: 9, Indels: 3
        0.83            0.13        0.04

Matches are distributed among these distances:
  57    6  0.10
  58   50  0.86
  59    2  0.03

ACGTcount: A:0.33, C:0.03, G:0.21, T:0.44


Consensus pattern (58 bp):   
GATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATACTCATGTGACTAATGT
Done.