Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007560.1 Kokia drynarioides strain JFW-HI SEQ_122188, 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: 15155
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33


Found at i:2579 original size:12 final size:12

Alignment explanation


    Indices: 2562--2605  Score: 54
    Period size: 12  Copynumber: 3.7  Consensus size: 12

       2552 GGAGGGGAAG

                        
       2562 GAAGAAGAGAAA
          1 GAAGAAGAGAAA

                        
       2574 GAAGAAGA-AAA
          1 GAAGAAGAGAAA

                 *       
       2585 GAAAGGAGAGAAA
          1 G-AAGAAGAGAAA

              *     
       2598 GAGGAAGA
          1 GAAGAAGA

       2606 TTTTGTTGCA


Statistics
Matches: 27,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  11    4  0.15
  12   19  0.70
  13    4  0.15

ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00


Consensus pattern (12 bp):   
GAAGAAGAGAAA

Found at i:8709 original size:41 final size:41

Alignment explanation


    Indices: 8664--8745  Score: 146
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       8654 AAAATTACTT

                                         *           
       8664 ATTTTAATTACGTAAGAACATTCTCATAAGCTTTTAATCAA
          1 ATTTTAATTACGTAAGAACATTCTCATAAACTTTTAATCAA

                      *                              
       8705 ATTTTAATTATGTAAGAACATTCTCATAAACTTTTAATCAA
          1 ATTTTAATTACGTAAGAACATTCTCATAAACTTTTAATCAA

       8746 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:12133 original size:36 final size:36

Alignment explanation


    Indices: 12079--12220  Score: 169
    Period size: 36  Copynumber: 3.9  Consensus size: 36

      12069 CTGTTATGAA

                  *                             
      12079 AGTAAACATGTGGGTATGTTATTCATGCCATGTGAC
          1 AGTAAATATGTGGGTATGTTATTCATGCCATGTGAC

                    *   **            *         *
      12115 AGTAAATACGTGAATATGTTATTCATACCA-GATGAT
          1 AGTAAATATGTGGGTATGTTATTCATGCCATG-TGAC

                                    *       *   
      12151 AGTAAATATGTGGGTATGTTATTCCTGCCATGAGAC
          1 AGTAAATATGTGGGTATGTTATTCATGCCATGTGAC

            *     *                   *       
      12187 CGTAAAAATGTGGGTATGTTATTCATTCCATGTG
          1 AGTAAATATGTGGGTATGTTATTCATGCCATGTG

      12221 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:12205 original size:72 final size:72

Alignment explanation


    Indices: 12074--12212  Score: 197
    Period size: 72  Copynumber: 1.9  Consensus size: 72

      12064 GATGACTGTT

                                                 *         *                 
      12074 ATGAAAGTAAACATGTGGGTATGTTATTCATGCCATGTGACAGTAAATACGTGAATATGTTATTC
          1 ATGAAAGTAAACATGTGGGTATGTTATTCATGCCATGAGACAGTAAAAACGTGAATATGTTATTC

                   
      12139 ATACCAG
         66 ATACCAG

                *      *                 *           *       *   **          
      12146 ATGATAGTAAATATGTGGGTATGTTATTCCTGCCATGAGACCGTAAAAATGTGGGTATGTTATTC
          1 ATGAAAGTAAACATGTGGGTATGTTATTCATGCCATGAGACAGTAAAAACGTGAATATGTTATTC

              
      12211 AT
         66 AT

      12213 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:12749 original size:58 final size:58

Alignment explanation


    Indices: 12642--12767  Score: 148
    Period size: 58  Copynumber: 2.2  Consensus size: 58

      12632 GTGATTATTA

                                                      * *             
      12642 GATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTTATGTGACTAATGT
          1 GATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATACTCATGTGACTAATGT

                                  *    *           **           *  *   
      12700 GATTAAATGTGATTAATATGTGTTGTGTTAAATGCTT-ATGTACTCATGTGATTATTGT
          1 GATTAAATGTGATTAATATGTGATGTGATAAATG-TTGAAATACTCATGTGACTAATGT

            *          
      12758 AATT-AATGTG
          1 GATTAAATGTG

      12768 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.