Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008000.1 Hibiscus syriacus cultivar Beakdansim tig00110457_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: 1646480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 9 of 9

Found at i:1625437 original size:88 final size:88

Alignment explanation


    Indices: 1625332--1625495  Score: 283
    Period size: 88  Copynumber: 1.9  Consensus size: 88

    1625322 AAATATGTCA

                        *         *                                          
    1625332 ATATAAGTACTATCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
          1 ATATAAGTACTACCTATTACATCATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT

                                   
    1625397 CCAGTTAAATGTCTATTTTTTTT
         66 CCAGTTAAATGTCTATTTTTTTT

                    *                                                  *     
    1625420 ATATAAGTGCTACCTATTACATCATATAAGCGCTACCTAATATGTTATTGTACTTAATACTATTT
          1 ATATAAGTACTACCTATTACATCATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT

              *        
    1625485 CCGGTTAAATG
         66 CCAGTTAAATG

    1625496 ATATAACATA


Statistics
Matches: 71,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  88   71  1.00

ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43


Consensus pattern (88 bp):   
ATATAAGTACTACCTATTACATCATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
CCAGTTAAATGTCTATTTTTTTT

Found at i:1631593 original size:14 final size:16

Alignment explanation


    Indices: 1631569--1631600  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

    1631559 AATTATAAAT

                            
    1631569 AGTATATATGT-TTCG
          1 AGTATATATGTCTTCG

                            
    1631584 AGTA-ATATGTCTTCG
          1 AGTATATATGTCTTCG

              
    1631599 AG
          1 AG

    1631601 AAGTATTGCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    6  0.38
  15   10  0.62

ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41


Consensus pattern (16 bp):   
AGTATATATGTCTTCG

Found at i:1635425 original size:105 final size:105

Alignment explanation


    Indices: 1635208--1635774  Score: 904
    Period size: 105  Copynumber: 5.4  Consensus size: 105

    1635198 GTATTGTTCC

                         *   *                                  *    *       
    1635208 GGAGTCCAATATCATTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTCGGTTGACA
          1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTCTGTTGACA

            **                               ***     
    1635273 GTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTATACTGTCT
         65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT

            **                                                               
    1635314 TAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTCTGTTGACAA
          1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTCTGTTGACAA

                                                    
    1635379 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
         66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT

                                               *       *                     
    1635419 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT-AGGATTGAGAAATGGT-TGTTGAC
          1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGAGAAAT-GTCTGTTGAC

                                                      
    1635482 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
         64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT

              *                                                    *         
    1635524 GGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
          1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTCTGTTGACAA

                                           *        
    1635589 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
         66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT

                                                          *        * *       
    1635629 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAATGTTTATTGACAA
          1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTCTGTTGACAA

                *                          *        
    1635694 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
         66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT

                                                     
    1635734 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
          1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG

    1635775 GGTAAAACCT


Statistics
Matches: 434,  Mismatches: 23, Indels: 9
        0.93            0.05        0.02

Matches are distributed among these distances:
 104    3  0.01
 105  381  0.88
 106   50  0.12

ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33


Consensus pattern (105 bp):   
GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTCTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT

Found at i:1636579 original size:46 final size:46

Alignment explanation


    Indices: 1636522--1636613  Score: 114
    Period size: 45  Copynumber: 2.0  Consensus size: 46

    1636512 TTTTCCCTTC

                            *     *      *  *              
    1636522 TTTTTTCTTTTCTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAA
          1 TTTTTTCTTTTC-CAACTTAGGACGCCCTCTCAGGTTTTCACCCTAA

                         *                          *     
    1636569 TTTTTT-TTTTCCGACTTAGGACGCCCTCTCAGGTTTTCATCCTAA
          1 TTTTTTCTTTTCCAACTTAGGACGCCCTCTCAGGTTTTCACCCTAA

    1636614 GCGAAGTATT


Statistics
Matches: 39,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  45   28  0.72
  46    5  0.13
  47    6  0.15

ACGTcount: A:0.14, C:0.26, G:0.14, T:0.46


Consensus pattern (46 bp):   
TTTTTTCTTTTCCAACTTAGGACGCCCTCTCAGGTTTTCACCCTAA

Done.