Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01005242.1 Hibiscus syriacus cultivar Beakdansim tig00011864_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: 49195
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:6752 original size:103 final size:103

Alignment explanation


    Indices: 6573--6779  Score: 351
    Period size: 103  Copynumber: 2.0  Consensus size: 103

       6563 CATCACCAAA

                        *          *                                  *      
       6573 ATCATTGCTCGTTGACTCCAGAGTATCATCCCGCTCCTTGTTTCTCCGAACCAAACAAGCTTCAT
          1 ATCATTGCTCGTCGACTCCAGAGCATCATCCCGCTCCTTGTTTCTCCGAACCAAACAAACTTCAT

                  *                               
       6638 TCTGGGTCGCTCTATCACTAAAAATATTGTTATCAACC
         66 TCTGGGCCGCTCTATCACTAAAAATATTGTTATCAACC

                   *                      *                                  
       6676 ATCATTGTTCGTCGACTCCAGAGCATCATCTCGCTCCTTGTTTCTCCGAACCAAACAAACTTCAT
          1 ATCATTGCTCGTCGACTCCAGAGCATCATCCCGCTCCTTGTTTCTCCGAACCAAACAAACTTCAT

                               *                  
       6741 TCTGGGCCGCTCTATCACTGAAAATATTGTTATCAACC
         66 TCTGGGCCGCTCTATCACTAAAAATATTGTTATCAACC

             
       6779 A
          1 A

       6780 GGAAATCATC


Statistics
Matches: 97,  Mismatches: 7, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 103   97  1.00

ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31


Consensus pattern (103 bp):   
ATCATTGCTCGTCGACTCCAGAGCATCATCCCGCTCCTTGTTTCTCCGAACCAAACAAACTTCAT
TCTGGGCCGCTCTATCACTAAAAATATTGTTATCAACC

Found at i:8916 original size:16 final size:16

Alignment explanation


    Indices: 8895--8936  Score: 57
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       8885 TGAGAAAAAT

                            
       8895 TTAATTTAAATTTAAA
          1 TTAATTTAAATTTAAA

                     *      
       8911 TTAATTTAATTTTAAA
          1 TTAATTTAAATTTAAA

            *         
       8927 ATAATGTTAA
          1 TTAAT-TTAA

       8937 TAAATAATTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  16   19  0.83
  17    4  0.17

ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50


Consensus pattern (16 bp):   
TTAATTTAAATTTAAA

Found at i:12596 original size:2 final size:2

Alignment explanation


    Indices: 12589--12630  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

      12579 TCATAACTTC

                                                                          
      12589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      12631 TTTAACATAG


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:22581 original size:20 final size:20

Alignment explanation


    Indices: 22558--22620  Score: 62
    Period size: 21  Copynumber: 3.2  Consensus size: 20

      22548 TATTAATTAA

                                
      22558 TTAAAATCATATATAATCGT
          1 TTAAAATCATATATAATCGT

                          * *     
      22578 TTAAAAAT-ATCATGTTAT-G-
          1 TT-AAAATCAT-ATATAATCGT

                                
      22597 TT-AAATCATATATAATCGT
          1 TTAAAATCATATATAATCGT

                 
      22616 TTAAA
          1 TTAAA

      22621 CTTAATGGTA


Statistics
Matches: 33,  Mismatches: 4, Indels: 12
        0.67            0.08        0.24

Matches are distributed among these distances:
  17    9  0.27
  18    3  0.09
  19    4  0.12
  20    7  0.21
  21   10  0.30

ACGTcount: A:0.44, C:0.08, G:0.06, T:0.41


Consensus pattern (20 bp):   
TTAAAATCATATATAATCGT

Found at i:22619 original size:19 final size:19

Alignment explanation


    Indices: 22561--22620  Score: 54
    Period size: 17  Copynumber: 3.2  Consensus size: 19

      22551 TAATTAATTA

                               
      22561 AAATCATATATAATCGTTT
          1 AAATCATATATAATCGTTT

                        * *       
      22580 AAAAAT-ATCATGTTAT-G-TT
          1 --AAATCAT-ATATAATCGTTT

                               
      22599 AAATCATATATAATCGTTT
          1 AAATCATATATAATCGTTT

               
      22618 AAA
          1 AAA

      22621 CTTAATGGTA


Statistics
Matches: 31,  Mismatches: 4, Indels: 10
        0.69            0.09        0.22

Matches are distributed among these distances:
  17    9  0.29
  18    3  0.10
  19    7  0.23
  20    3  0.10
  21    9  0.29

ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40


Consensus pattern (19 bp):   
AAATCATATATAATCGTTT

Found at i:35924 original size:17 final size:19

Alignment explanation


    Indices: 35888--35924  Score: 51
    Period size: 17  Copynumber: 2.1  Consensus size: 19

      35878 CAAAGACCAA

                               
      35888 TCATATGATGATTATATTG
          1 TCATATGATGATTATATTG

                     *         
      35907 TCATA-GATTATT-TATTG
          1 TCATATGATGATTATATTG

             
      35924 T
          1 T

      35925 ATTTATTAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  17    6  0.35
  18    6  0.35
  19    5  0.29

ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51


Consensus pattern (19 bp):   
TCATATGATGATTATATTG
Done.