Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01006517.1 Hibiscus syriacus cultivar Beakdansim tig00015872_pilon, 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: 37020
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:1652 original size:24 final size:22

Alignment explanation


    Indices: 1604--1652  Score: 55
    Period size: 24  Copynumber: 2.1  Consensus size: 22

       1594 TGGAGTGCAA

                                * 
       1604 AAAGAAAAGAAAAGACAAAACG
          1 AAAGAAAAGAAAAGACAAAAAG

                                     
       1626 AAAGAAATCAGAAAAGA-AGAAAAG
          1 AAAGAAA--AGAAAAGACA-AAAAG

               
       1650 AAA
          1 AAA

       1653 AGTCAAAAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  22    7  0.30
  23    1  0.04
  24   15  0.65

ACGTcount: A:0.73, C:0.06, G:0.18, T:0.02


Consensus pattern (22 bp):   
AAAGAAAAGAAAAGACAAAAAG

Found at i:6283 original size:24 final size:24

Alignment explanation


    Indices: 6256--6355  Score: 85
    Period size: 24  Copynumber: 4.2  Consensus size: 24

       6246 AGATATCAAA

                     *              
       6256 ATCAAAACATAATTCAGATCAGAT
          1 ATCAAAACAGAATTCAGATCAGAT

                *        *   * *     
       6280 ATCAGAACAGAATCCAGGTTAGGA-
          1 ATCAAAACAGAATTCAGATCA-GAT

                *    * *            
       6304 ATCAGAACATATTTCAGATCAGAT
          1 ATCAAAACAGAATTCAGATCAGAT

            *               *      *
       6328 GTCAAAACAGAATTCAAATCAGAA
          1 ATCAAAACAGAATTCAGATCAGAT

                
       6352 ATCA
          1 ATCA

       6356 GATAAAATTC


Statistics
Matches: 57,  Mismatches: 17, Indels: 4
        0.73            0.22        0.05

Matches are distributed among these distances:
  23    2  0.04
  24   53  0.93
  25    2  0.04

ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22


Consensus pattern (24 bp):   
ATCAAAACAGAATTCAGATCAGAT

Found at i:6355 original size:48 final size:48

Alignment explanation


    Indices: 6250--6357  Score: 128
    Period size: 48  Copynumber: 2.3  Consensus size: 48

       6240 AAACGGAGAT

                       *                       *           *
       6250 ATCA-AAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
          1 ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA

            * *  *            *            *            *   
       6297 GTTAGGAATCAGAACATATTTCAGATCAGATGTCAAAACAGAATTCAA
          1 ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA

                         
       6345 ATCAGAAATCAGA
          1 ATCAGAAATCAGA

       6358 TAAAATTCAT


Statistics
Matches: 48,  Mismatches: 12, Indels: 1
        0.79            0.20        0.02

Matches are distributed among these distances:
  47    2  0.04
  48   46  0.96

ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21


Consensus pattern (48 bp):   
ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA

Found at i:7516 original size:17 final size:18

Alignment explanation


    Indices: 7483--7516  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       7473 TCCATTCTGT

                 *            
       7483 CTTATTATTTAATTCCAA
          1 CTTATCATTTAATTCCAA

                             
       7501 CTTATCATTT-ATTCCA
          1 CTTATCATTTAATTCCA

       7517 GACCTTTCAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    6  0.40
  18    9  0.60

ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50


Consensus pattern (18 bp):   
CTTATCATTTAATTCCAA

Found at i:8808 original size:18 final size:18

Alignment explanation


    Indices: 8787--8833  Score: 69
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       8777 CGTCGGTCAA

                          *    
       8787 CGGGTCGGGTCAA-TGGTT
          1 CGGGTCGGGTCAACAGG-T

                              
       8805 CGGGTCGGGTCAACAGGT
          1 CGGGTCGGGTCAACAGGT

                       
       8823 CGGGTCGGGTC
          1 CGGGTCGGGTC

       8834 GGGTTGTGAC


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  18   25  0.93
  19    2  0.07

ACGTcount: A:0.11, C:0.21, G:0.47, T:0.21


Consensus pattern (18 bp):   
CGGGTCGGGTCAACAGGT

Found at i:22264 original size:15 final size:15

Alignment explanation


    Indices: 22236--22299  Score: 67
    Period size: 15  Copynumber: 4.2  Consensus size: 15

      22226 ATTTTAAAAT

                             
      22236 TAATGAAAGTAAATAAA
          1 TAATGAAA--AAATAAA

                *          
      22253 TAATAAAAAAATAAA
          1 TAATGAAAAAATAAA

              *    *       
      22268 TATTGAATAAA-AAA
          1 TAATGAAAAAATAAA

                     *     
      22282 TAATGAAAAGATAAA
          1 TAATGAAAAAATAAA

               
      22297 TAA
          1 TAA

      22300 AGCAAATAAA


Statistics
Matches: 39,  Mismatches: 7, Indels: 4
        0.78            0.14        0.08

Matches are distributed among these distances:
  14   11  0.28
  15   21  0.54
  17    7  0.18

ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23


Consensus pattern (15 bp):   
TAATGAAAAAATAAA
Done.