Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01002662.1 Hibiscus syriacus cultivar Beakdansim tig00005463_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: 218144
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


File 2 of 2

Found at i:210582 original size:36 final size:38

Alignment explanation


    Indices: 210537--210745  Score: 173
    Period size: 36  Copynumber: 5.7  Consensus size: 38

     210527 TGTCTCGAGC

                              *            *      
     210537 GAGACAAATT-TTGTTT-TAAGGAAAACAATTTCAAGT
          1 GAGACAAATTGTTGTTTCGAAGGAAAACAATCTCAAGT

                *      *         *      **    *  *
     210573 GAGATAAATTGCTGTTTCGAATG-AAACTGTCTCGAGC
          1 GAGACAAATTGTTGTTTCGAAGGAAAACAATCTCAAGT

                              *   *               
     210610 GAGACAAATT-TTGTTT-TAAGAAAAACAATCTCAAGT
          1 GAGACAAATTGTTGTTTCGAAGGAAAACAATCTCAAGT

                *      *         *      **    *  *
     210646 GAGATAAATTGCTGTTTCGAATG-AAACTGTCTCGAGC
          1 GAGACAAATTGTTGTTTCGAAGGAAAACAATCTCAAGT

                              *   *               
     210683 GAGACAAATT-TTGTTT-TAAGAAAAACAATCTCAAGT
          1 GAGACAAATTGTTGTTTCGAAGGAAAACAATCTCAAGT

                *                      
     210719 GAGATAAATTGTTGTTTCGAAGGAAAA
          1 GAGACAAATTGTTGTTTCGAAGGAAAA

     210746 TGTTTAATAA


Statistics
Matches: 126,  Mismatches: 39, Indels: 14
        0.70            0.22        0.08

Matches are distributed among these distances:
  35    4  0.03
  36   57  0.45
  37   53  0.42
  38   12  0.10

ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31


Consensus pattern (38 bp):   
GAGACAAATTGTTGTTTCGAAGGAAAACAATCTCAAGT

Found at i:210616 original size:73 final size:73

Alignment explanation


    Indices: 210512--210744  Score: 421
    Period size: 73  Copynumber: 3.2  Consensus size: 73

     210502 TGGAAATTTA

                    *                                    *        *          
     210512 TGTTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGGAAAACAATTTCAAGTGAGA
          1 TGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA

                    
     210577 TAAATTGC
         66 TAAATTGC

                                                                             
     210585 TGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
          1 TGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA

                    
     210650 TAAATTGC
         66 TAAATTGC

                                                                             
     210658 TGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
          1 TGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA

                   *
     210723 TAAATTGT
         66 TAAATTGC

                     *    
     210731 TGTTTCGAAGGAAA
          1 TGTTTCGAATGAAA

     210745 ATGTTTAATA


Statistics
Matches: 155,  Mismatches: 5, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  73  155  1.00

ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31


Consensus pattern (73 bp):   
TGTTTCGAATGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAATTGC

Found at i:211036 original size:166 final size:165

Alignment explanation


    Indices: 210743--211064  Score: 506
    Period size: 166  Copynumber: 1.9  Consensus size: 165

     210733 TTTCGAAGGA

                                                                    *        
     210743 AAATGTTTAATAAGTAAAAAACTAAGAAAAATAGTTTTCTTACTTTTCAACAATTTTATTTTCAG
          1 AAATGTTTAATAAGTAAAAAACTAAGAAAAATAGTTTTCTTACTTTTCAACAATTTCATTTTCAG

                   **           *                                  *         
     210808 AAAAGATTGAATGAGAAACTTTGGAAATCGTTTTCTCATTATGTTTCAAGATAACCTGTTGATTG
         66 AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTCAAGATAACATGTTGATTG

                     *         *               
     210873 GGTAACATGTCCCAATCTCCAGATAAGGTTGTTGG
        131 GGTAACATGCCCCAATCTCAAGATAAGGTTGTTGG

                                              *                              
     210908 AAATAGTTTAATAAGTAAAAAAACTAAG-AAAATCGTTTTCTTACTTTTCAACAATTTCATTTT-
          1 AAAT-GTTTAATAAGT-AAAAAACTAAGAAAAATAGTTTTCTTACTTTTCAACAATTTCATTTTC

                                                              *              
     210971 AGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTTTGAA-ATAACATGTTG
         64 AGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATG--TTTCAAGATAACATGTTG

                                          
     211035 ATTGGGTAACATGCCCCAATCTCAAGATAA
        127 ATTGGGTAACATGCCCCAATCTCAAGATAA

     211065 TGCTCATTCT


Statistics
Matches: 144,  Mismatches: 9, Indels: 7
        0.90            0.06        0.04

Matches are distributed among these distances:
 165   46  0.32
 166   82  0.57
 167   16  0.11

ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35


Consensus pattern (165 bp):   
AAATGTTTAATAAGTAAAAAACTAAGAAAAATAGTTTTCTTACTTTTCAACAATTTCATTTTCAG
AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATGTTTCAAGATAACATGTTGATTG
GGTAACATGCCCCAATCTCAAGATAAGGTTGTTGG

Found at i:211615 original size:21 final size:21

Alignment explanation


    Indices: 211567--211644  Score: 75
    Period size: 22  Copynumber: 3.6  Consensus size: 21

     211557 CATAAAGTTT

                           *      
     211567 TCATCTTTGAAAAGAGAATCTA
          1 TCATCTTT-AAAAGAAAATCTA

             *                * *
     211589 TTATCTTTAAAAGAAAATTTG
          1 TCATCTTTAAAAGAAAATCTA

                    *  **         
     211610 TCATCTCTGAAGTGAAAATCTA
          1 TCATCT-TTAAAAGAAAATCTA

                         
     211632 TCATCTTTAAAAG
          1 TCATCTTTAAAAG

     211645 TGTAGATGTA


Statistics
Matches: 42,  Mismatches: 13, Indels: 3
        0.72            0.22        0.05

Matches are distributed among these distances:
  21   19  0.45
  22   23  0.55

ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36


Consensus pattern (21 bp):   
TCATCTTTAAAAGAAAATCTA

Done.