Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01009308.1 Hibiscus syriacus cultivar Beakdansim tig00113044_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: 172755
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


File 2 of 2

Found at i:166511 original size:19 final size:19

Alignment explanation


    Indices: 166484--166522  Score: 60
    Period size: 19  Copynumber: 2.1  Consensus size: 19

     166474 TTAATTTTTT

                *              
     166484 AAAATAATAATTAAATTTA
          1 AAAAAAATAATTAAATTTA

                         *     
     166503 AAAAAAATAATTATATTTA
          1 AAAAAAATAATTAAATTTA

             
     166522 A
          1 A

     166523 GATTAATGAT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  19   18  1.00

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


Consensus pattern (19 bp):   
AAAAAAATAATTAAATTTA

Found at i:169741 original size:107 final size:107

Alignment explanation


    Indices: 169563--169839  Score: 439
    Period size: 107  Copynumber: 2.6  Consensus size: 107

     169553 AACAATTTGG

                 *                    **                                     
     169563 TATCAATAAATCTATTCTAATAACGTGTAG-GATCATCTTGTTCACTGATAGTGCATAACATTAT
          1 TATCACTAAATCTATTCTAATAACG-CCAGTGATCATCTTGTTCACTGATAGTGCATAACATTAT

                          *                            
     169627 ATACCATCAGTCCATATCAATATTTCACTCATAAACAACTACC
         65 ATACCATCAGTCCAGATCAATATTTCACTCATAAACAACTACC

                                                                    *        
     169670 TATCACTAAATCTATTCTAATAACGCCAGTGATCATCTTGTTCACTGATAGTGCATTACATTATA
          1 TATCACTAAATCTATTCTAATAACGCCAGTGATCATCTTGTTCACTGATAGTGCATAACATTATA

             *               *                        
     169735 TGCCATCAGTCCAGATCGATATTTCACTCATAAACAACTACC
         66 TACCATCAGTCCAGATCAATATTTCACTCATAAACAACTACC

              *                                             *  *      *    
     169777 TACCACTAAATCTATTCTAATAACGCCAGTGATCATCTTGTTCACTGAAAGAGCATAAAATTA
          1 TATCACTAAATCTATTCTAATAACGCCAGTGATCATCTTGTTCACTGATAGTGCATAACATTA

     169840 ACCCAAATCA


Statistics
Matches: 157,  Mismatches: 12, Indels: 2
        0.92            0.07        0.01

Matches are distributed among these distances:
 106    2  0.01
 107  155  0.99

ACGTcount: A:0.35, C:0.22, G:0.10, T:0.32


Consensus pattern (107 bp):   
TATCACTAAATCTATTCTAATAACGCCAGTGATCATCTTGTTCACTGATAGTGCATAACATTATA
TACCATCAGTCCAGATCAATATTTCACTCATAAACAACTACC

Found at i:170276 original size:105 final size:107

Alignment explanation


    Indices: 169999--170510  Score: 487
    Period size: 107  Copynumber: 4.9  Consensus size: 107

     169989 TATTCTAAGT

                         *           *          **                   *     * 
     169999 TTCTAATAAAGCGGGTGATCATCTTGTTCACTGATGGGGCATAAAATTATATACAGTTAGTCCAT
          1 TTCTAATAAAGCGCGTGATCATCTTATTCACTGATGATGCATAAAATTATATACAGTCAGTCCGT

                *               *     * *           * 
     170064 ATCGGTATTTCACTCGTAAATAA-TATGCATCACTAAATCCA
         66 ATCGATATTTCACTCGTAAACAATTACGTATCACTAAATCTA

                           *           *  *                *                 
     170105 TTCTAATAACA-CGCATGATCATCTT-GTCGCTGAT-AGTGCAT-AACTTATATA-ATGTCAGTC
          1 TTCTAATAA-AGCGCGTGATCATCTTATTCACTGATGA-TGCATAAAATTATATACA-GTCAGTC

             *                                          * 
     170165 CATATCGATATTTCACTCGTGAAA-AATTACGTATCACT-AATCAA
         63 CGTATCGATATTTCACTCGT-AAACAATTACGTATCACTAAATCTA

                    ** * *                                          *        
     170209 TTCTAATAGCGTGTGTGATCATCTTATTCACTGATGATGCAT-AAATTATATACAGCCAGTCCGT
          1 TTCTAATAAAGCGCGTGATCATCTTATTCACTGATGATGCATAAAATTATATACAGTCAGTCCGT

                           *           *    *         
     170273 ATCGATATTTCACTCATAAACAATTACATATCGCTAAATCTA
         66 ATCGATATTTCACTCGTAAACAATTACGTATCACTAAATCTA

                    *  *            **     *               *      * *        
     170315 TTCTAATAGAGAGCGTGATCATCTCGTTCACCGATGATGCATAAAATCATATACCGACAGT-CGA
          1 TTCTAATAAAGCGCGTGATCATCTTATTCACTGATGATGCATAAAATTATATACAGTCAGTCCG-

                 *                     *                
     170379 TATCGGTATTTCACT-GATAAACAATTTCGTATCACTAAATCTA
         65 TATCGATATTTCACTCG-TAAACAATTACGTATCACTAAATCTA

                  *      *                                        **         
     170422 TTCTAACAAAGCGAGTGATCATCTTATTCACTGATAGA-GCATAAAATTATATATTGTCAGT-CG
          1 TTCTAATAAAGCGCGTGATCATCTTATTCACTGAT-GATGCATAAAATTATATACAGTCAGTCCG

                             *          
     170485 ATATCGAT-TTTCACTCATAAA-AATTA
         65 -TATCGATATTTCACTCGTAAACAATTA

     170511 AAGCAAACAA


Statistics
Matches: 336,  Mismatches: 54, Indels: 33
        0.79            0.13        0.08

Matches are distributed among these distances:
 103    1  0.00
 104   63  0.19
 105   84  0.25
 106   77  0.23
 107  109  0.32
 108    2  0.01

ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33


Consensus pattern (107 bp):   
TTCTAATAAAGCGCGTGATCATCTTATTCACTGATGATGCATAAAATTATATACAGTCAGTCCGT
ATCGATATTTCACTCGTAAACAATTACGTATCACTAAATCTA

Found at i:172546 original size:18 final size:18

Alignment explanation


    Indices: 172512--172546  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

     172502 GAAGTCATAC

                  *     *     
     172512 TACAAATAAAAATAAAAT
          1 TACAAAAAAAAAAAAAAT

                             
     172530 TACAAAAAAAAAAAAAA
          1 TACAAAAAAAAAAAAAA

     172547 ACAGAAATTA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14


Consensus pattern (18 bp):   
TACAAAAAAAAAAAAAAT

Done.