Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01000119.1 Hibiscus syriacus cultivar Beakdansim tig00000216_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: 10483
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32


Found at i:1633 original size:43 final size:43

Alignment explanation


    Indices: 1489--1639  Score: 164
    Period size: 42  Copynumber: 3.6  Consensus size: 43

       1479 TAATTAAATT

                         *    *     *                  
       1489 AAGTGAGATTGAATAAATGAGGGGTCTC-ATTATAAAAGTAAA
          1 AAGTGAGATTGAAAAAATTAGGGGCCTCAATTATAAAAGTAAA

                   *  *           *  *           *   * 
       1531 AAGTGAGCTTAAAAAAATTAGGAGCTTCAA-TATAAAGGTAGA
          1 AAGTGAGATTGAAAAAATTAGGGGCCTCAATTATAAAAGTAAA

               *      *                          *     
       1573 AAGCGAGATTTAAAAAATTAGGGGCCTCAATTATAAACGTAAA
          1 AAGTGAGATTGAAAAAATTAGGGGCCTCAATTATAAAAGTAAA

                 *                   
       1616 AAGTGGGATTGAAAAAATT-GGGGC
          1 AAGTGAGATTGAAAAAATTAGGGGC

       1640 ATCGAATATC


Statistics
Matches: 88,  Mismatches: 19, Indels: 4
        0.79            0.17        0.04

Matches are distributed among these distances:
  42   61  0.69
  43   27  0.31

ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24


Consensus pattern (43 bp):   
AAGTGAGATTGAAAAAATTAGGGGCCTCAATTATAAAAGTAAA

Found at i:1648 original size:85 final size:84

Alignment explanation


    Indices: 1493--1648  Score: 197
    Period size: 85  Copynumber: 1.8  Consensus size: 84

       1483 TAAATTAAGT

                     *          *                        *                 * 
       1493 GAGATTGAATAAATGAGGGGTCTCATTATAAAAGTAAAAAGTGAGCTTAAAAAAATTAGGAGCTT
          1 GAGATTGAAAAAATGAGGGGCCTCATTATAAAAGTAAAAAGTGAGATTAAAAAAATTAGGAGCAT

                               
       1558 CAATATAAAGGTAGAAAGC
         66 CAATATAAAGGTAGAAAGC

                  *       *                  *          *    *           *   
       1577 GAGATTTAAAAAATTAGGGGCCTCAATTATAAACGTAAAAAGTGGGATTGAAAAAATT-GGGGCA
          1 GAGATTGAAAAAATGAGGGGCCTC-ATTATAAAAGTAAAAAGTGAGATTAAAAAAATTAGGAGCA

                    
       1641 TCGAATAT
         65 TC-AATAT

       1649 CGATTATTAA


Statistics
Matches: 60,  Mismatches: 10, Indels: 3
        0.82            0.14        0.04

Matches are distributed among these distances:
  84   26  0.43
  85   34  0.57

ACGTcount: A:0.45, C:0.08, G:0.23, T:0.24


Consensus pattern (84 bp):   
GAGATTGAAAAAATGAGGGGCCTCATTATAAAAGTAAAAAGTGAGATTAAAAAAATTAGGAGCAT
CAATATAAAGGTAGAAAGC

Found at i:2141 original size:23 final size:23

Alignment explanation


    Indices: 2106--2152  Score: 60
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       2096 TATTGCTAAC

                *                   
       2106 AAAATTAAAAAT-AATTATATTTT
          1 AAAAATAAAAATAAATT-TATTTT

                    *              
       2129 AAAAATAATAATAAATTTATTTT
          1 AAAAATAAAAATAAATTTATTTT

             
       2152 A
          1 A

       2153 TTTAAAATAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  23   17  0.81
  24    4  0.19

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (23 bp):   
AAAAATAAAAATAAATTTATTTT

Found at i:5790 original size:2 final size:2

Alignment explanation


    Indices: 5783--5834  Score: 95
    Period size: 2  Copynumber: 26.0  Consensus size: 2

       5773 TGTTCTTGAA

                                                                      *   
       5783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                          
       5825 AT AT AT AT AT
          1 AT AT AT AT AT

       5835 GTTTCTATAT


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   2   48  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:9603 original size:18 final size:19

Alignment explanation


    Indices: 9559--9603  Score: 51
    Period size: 18  Copynumber: 2.5  Consensus size: 19

       9549 CAATAAGTGT

                               
       9559 TCTTGAAA-GAAAAATGAA
          1 TCTTGAAATGAAAAATGAA

             *                *
       9577 TATTG-AATGAAAAAT-AG
          1 TCTTGAAATGAAAAATGAA

                      
       9594 TCTTGAAATG
          1 TCTTGAAATG

       9604 CTCAAACTTG


Statistics
Matches: 22,  Mismatches: 3, Indels: 4
        0.76            0.10        0.14

Matches are distributed among these distances:
  17    7  0.32
  18   15  0.68

ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29


Consensus pattern (19 bp):   
TCTTGAAATGAAAAATGAA
Done.