Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008419.1 Hibiscus syriacus cultivar Beakdansim tig00111199_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: 1038719
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


File 5 of 5

Found at i:1006602 original size:61 final size:63

Alignment explanation


    Indices: 1006516--1006661  Score: 176
    Period size: 62  Copynumber: 2.4  Consensus size: 63

    1006506 ATGCACATTC

                                         *            *         *          
    1006516 ATAAGTGCATCGATGCATTCCTTTAAAA-GAACATCGAATGCCTTTGATGCATCGATGCATAG
          1 ATAAGTGCATCGATGCATTCCTTTAAAATAAACATCGAATGCATTTGATGCACCGATGCATAG

                                                           *             *  
    1006578 ATAA-TGCATCGATGCA-TCCTTTTAAAATAAACATCGAATGCATTTTATGCACCGATGCACA-
          1 ATAAGTGCATCGATGCATTCC-TTTAAAATAAACATCGAATGCATTTGATGCACCGATGCATAG

                *              *    
    1006639 AGT-GGTGCATCGATGCATACCTT
          1 A-TAAGTGCATCGATGCATTCCTT

    1006662 CATTGAAAGA


Statistics
Matches: 72,  Mismatches: 7, Indels: 10
        0.81            0.08        0.11

Matches are distributed among these distances:
  60    3  0.04
  61   20  0.28
  62   47  0.65
  63    2  0.03

ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29


Consensus pattern (63 bp):   
ATAAGTGCATCGATGCATTCCTTTAAAATAAACATCGAATGCATTTGATGCACCGATGCATAG

Found at i:1007367 original size:29 final size:30

Alignment explanation


    Indices: 1007302--1007373  Score: 92
    Period size: 29  Copynumber: 2.4  Consensus size: 30

    1007292 GGTTCTTCGG

                 *    *               *   
    1007302 GACCTGTGGACAGTTACCGAGGATCTTTAT
          1 GACCTCTGGATAGTTACCGAGGATCTGTAT

                                  *     * 
    1007332 GACCTCTGGATAGTTACCG-GGGTCTGTGT
          1 GACCTCTGGATAGTTACCGAGGATCTGTAT

                         
    1007361 GACCTCTGGATAG
          1 GACCTCTGGATAG

    1007374 GTCCTTCGGG


Statistics
Matches: 37,  Mismatches: 5, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  29   20  0.54
  30   17  0.46

ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29


Consensus pattern (30 bp):   
GACCTCTGGATAGTTACCGAGGATCTGTAT

Found at i:1009436 original size:20 final size:20

Alignment explanation


    Indices: 1009411--1009453  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

    1009401 TCTAAGAGCC

                         *      
    1009411 CATTTAGGACCATTTAGATG
          1 CATTTAGGACCATATAGATG

                     *       *  
    1009431 CATTTAGGAGCATATAGTTG
          1 CATTTAGGACCATATAGATG

               
    1009451 CAT
          1 CAT

    1009454 GTGGTGGATT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35


Consensus pattern (20 bp):   
CATTTAGGACCATATAGATG

Found at i:1026549 original size:49 final size:48

Alignment explanation


    Indices: 1026458--1026631  Score: 206
    Period size: 49  Copynumber: 3.5  Consensus size: 48

    1026448 CCTAGTTGTA

                 *                                      *     
    1026458 AGTATATGTTAAGTGCTACACTTTTTTATTTTATTCACTTACATTGGTGT
          1 AGTATGTGTTAAGTGCTACAC-TTTTTATTTTATTCACTTACA-CGGTGT

                *                     *                 *    
    1026508 AGTACGTGTTAAGTGCTACACTTTTTGTTTTATTCACTTACACCAGTG-
          1 AGTATGTGTTAAGTGCTACACTTTTTATTTTATTCACTTACA-CGGTGT

                        *       *                *         * 
    1026556 AGTATGTGTTAATTGCTACATTTGTTTATTTTATTCATTTACACGGTAT
          1 AGTATGTGTTAAGTGCTACACTT-TTTATTTTATTCACTTACACGGTGT

                                 *     
    1026605 AAGTATGTGTTAAGTGCTACATTTTTT
          1 -AGTATGTGTTAAGTGCTACACTTTTT

    1026632 GTAGTATGAA


Statistics
Matches: 107,  Mismatches: 14, Indels: 7
        0.84            0.11        0.05

Matches are distributed among these distances:
  48   23  0.21
  49   43  0.40
  50   41  0.38

ACGTcount: A:0.24, C:0.13, G:0.16, T:0.48


Consensus pattern (48 bp):   
AGTATGTGTTAAGTGCTACACTTTTTATTTTATTCACTTACACGGTGT

Found at i:1028615 original size:20 final size:22

Alignment explanation


    Indices: 1028590--1028630  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

    1028580 TTGACTCGAA

                            *     
    1028590 CTCG-AAA-TCATGAACTGAAG
          1 CTCGAAAAGTCATGAAATGAAG

                                 
    1028610 CTCGAAAAGTCATGAAATGAA
          1 CTCGAAAAGTCATGAAATGAA

    1028631 AAAACCTTAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    4  0.22
  21    3  0.17
  22   11  0.61

ACGTcount: A:0.44, C:0.17, G:0.20, T:0.20


Consensus pattern (22 bp):   
CTCGAAAAGTCATGAAATGAAG


Done.