Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01006382.1 Hibiscus syriacus cultivar Beakdansim tig00015367_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: 49860
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:32554 original size:15 final size:16

Alignment explanation


    Indices: 32523--32553  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      32513 TGTTATAATT

                            
      32523 TTAATTTTTTTAAAAA
          1 TTAATTTTTTTAAAAA

                           
      32539 TTAATTTTTTTAAAA
          1 TTAATTTTTTTAAAA

      32554 TAAAACTAAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (16 bp):   
TTAATTTTTTTAAAAA

Found at i:37751 original size:67 final size:66

Alignment explanation


    Indices: 37604--37952  Score: 522
    Period size: 67  Copynumber: 5.2  Consensus size: 66

      37594 GTGACCTAAA

                     *                                    *        *         
      37604 CTAATTCAGGTTCAGCCTTTCGTTGTTGCTTTCTATCG--TAGAAGACCTTGCTCCGTGTGACAT
          1 CTAATTCAGCTTCAG-CTTTCGTTGTTGCTTTCTATCGCATA-AAGGCCTTGCTCAGTGTGACAT

               
      37667 GAG
         64 GAG

                     *          *                                            
      37670 CTAATTCAGGTTCAGTCTTTAGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG
          1 CTAATTCAGCTTCAG-CTTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG

              
      37735 AG
         65 AG

            *                                                  *             
      37737 ATAATTCAGCTTCAGCTTTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGTTCAGTGTGACATG
          1 CTAATTCAGCTTCAGC-TTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG

              
      37802 AG
         65 AG

            *                                                                
      37804 ATAATTCAGCTTCAGCTTTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG
          1 CTAATTCAGCTTCAGC-TTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG

              
      37869 AG
         65 AG

                       *   *    *                 *                          
      37871 CTAATTCAGCTCCAACCTTTTGTTGTTGCTTTCTATCGTATAAAGGCCTTGCTCAGTGTGACATG
          1 CTAATTCAGCTTC-AGCTTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATG

              
      37936 AG
         65 AG

                           
      37938 CTAATTCAGCTTCAG
          1 CTAATTCAGCTTCAG

      37953 GTTTTAGTTC


Statistics
Matches: 263,  Mismatches: 16, Indels: 8
        0.92            0.06        0.03

Matches are distributed among these distances:
  66   38  0.14
  67  221  0.84
  68    4  0.02

ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37


Consensus pattern (66 bp):   
CTAATTCAGCTTCAGCTTTCGTTGTTGCTTTCTATCGCATAAAGGCCTTGCTCAGTGTGACATGA
G

Found at i:43070 original size:106 final size:106

Alignment explanation


    Indices: 42885--43090  Score: 376
    Period size: 106  Copynumber: 1.9  Consensus size: 106

      42875 ATTCATCGCT

                                                                 *   *       
      42885 GCCGTCTCTGAAGGTAAGAGGTTTTCTCCCACCCTTGACATATATATTACTAGTTTTGTGTATTC
          1 GCCGTCTCTGAAGGTAAGAGGTTTTCTCCCACCCTTGACATATATATTACTAGATTTCTGTATTC

                                 *                   
      42950 TCAGACAGAATTAGCAAATTCGTAGAATAAATCTTATCTGA
         66 TCAGACAGAATTAGCAAATTCATAGAATAAATCTTATCTGA

                            *                                                
      42991 GCCGTCTCTGAAGGTACGAGGTTTTCTCCCACCCTTGACATATATATTACTAGATTTCTGTATTC
          1 GCCGTCTCTGAAGGTAAGAGGTTTTCTCCCACCCTTGACATATATATTACTAGATTTCTGTATTC

                                               
      43056 TCAGACAGAATTAGCAAATTCATAGAATAAATCTT
         66 TCAGACAGAATTAGCAAATTCATAGAATAAATCTT

      43091 CTTTGACTTG


Statistics
Matches: 96,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 106   96  1.00

ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34


Consensus pattern (106 bp):   
GCCGTCTCTGAAGGTAAGAGGTTTTCTCCCACCCTTGACATATATATTACTAGATTTCTGTATTC
TCAGACAGAATTAGCAAATTCATAGAATAAATCTTATCTGA
Done.