Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008727.1 Hibiscus syriacus cultivar Beakdansim tig00111794_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: 1388410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 8 of 8

Found at i:1356254 original size:14 final size:14

Alignment explanation


    Indices: 1356235--1356265  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

    1356225 CAAACATACT

                          
    1356235 ATAGTTGAAAATCA
          1 ATAGTTGAAAATCA

                          
    1356249 ATAGTTGAAAATCA
          1 ATAGTTGAAAATCA

               
    1356263 ATA
          1 ATA

    1356266 CAAATTTGAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29


Consensus pattern (14 bp):   
ATAGTTGAAAATCA

Found at i:1369805 original size:20 final size:19

Alignment explanation


    Indices: 1369762--1369808  Score: 58
    Period size: 20  Copynumber: 2.4  Consensus size: 19

    1369752 GCTATCTTTG

                      *  *   * 
    1369762 GTATCGATACTCAGGGTGA
          1 GTATCGATACCCAAGGTCA

                                
    1369781 GTATCGATACCCAAAGGTCA
          1 GTATCGATACCC-AAGGTCA

                    
    1369801 GTATCGAT
          1 GTATCGAT

    1369809 TCCATAGTTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  19   11  0.46
  20   13  0.54

ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26


Consensus pattern (19 bp):   
GTATCGATACCCAAGGTCA

Found at i:1374177 original size:27 final size:25

Alignment explanation


    Indices: 1374147--1374238  Score: 73
    Period size: 26  Copynumber: 3.6  Consensus size: 25

    1374137 AAAAATAAAG

                                        
    1374147 AAATGAGAGAGAAAAAG-TAAAAGTTAA
          1 AAATGAGAGAGAAAAAGCTAAAA--T-A

                  * *                 
    1374174 AAATGAAATAGAAAAAGCTAATAATA
          1 AAATGAGAGAGAAAAAGCTAA-AATA

                              *       
    1374200 AAA-GAGAGAAGAAAAAGTTAAAA-A
          1 AAATGAGAG-AGAAAAAGCTAAAATA

                      *    
    1374224 AAATTGAGAGGGAAA
          1 AAA-TGAGAGAGAAA

    1374239 TGGGTGATAG


Statistics
Matches: 54,  Mismatches: 6, Indels: 12
        0.75            0.08        0.17

Matches are distributed among these distances:
  24    4  0.07
  25    9  0.17
  26   20  0.37
  27   16  0.30
  28    3  0.06
  29    2  0.04

ACGTcount: A:0.64, C:0.01, G:0.21, T:0.14


Consensus pattern (25 bp):   
AAATGAGAGAGAAAAAGCTAAAATA

Found at i:1382392 original size:29 final size:29

Alignment explanation


    Indices: 1382355--1382421  Score: 107
    Period size: 29  Copynumber: 2.3  Consensus size: 29

    1382345 CATTTTATTT

                *                        
    1382355 TAATATTTGTTCTTATTTTATTTTATAAA
          1 TAATTTTTGTTCTTATTTTATTTTATAAA

                               *    *    
    1382384 TAATTTTTGTTCTTATTTTCTTTTGTAAA
          1 TAATTTTTGTTCTTATTTTATTTTATAAA

                     
    1382413 TAATTTTTG
          1 TAATTTTTG

    1382422 ATTTGATTTG


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  29   35  1.00

ACGTcount: A:0.25, C:0.04, G:0.06, T:0.64


Consensus pattern (29 bp):   
TAATTTTTGTTCTTATTTTATTTTATAAA

Found at i:1382430 original size:29 final size:29

Alignment explanation


    Indices: 1382355--1382430  Score: 91
    Period size: 29  Copynumber: 2.6  Consensus size: 29

    1382345 CATTTTATTT

                *        *               
    1382355 TAATATTTGTTCTTATTTTATTTTATAAA
          1 TAATTTTTGTTCTGATTTTATTTTATAAA

                         *     *    *    
    1382384 TAATTTTTGTTCTTATTTTCTTTTGTAAA
          1 TAATTTTTGTTCTGATTTTATTTTATAAA

                               
    1382413 TAATTTTTGATT-TGATTT
          1 TAATTTTTG-TTCTGATTT

    1382431 GTAGGGACCA


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  29   40  0.95
  30    2  0.05

ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64


Consensus pattern (29 bp):   
TAATTTTTGTTCTGATTTTATTTTATAAA

Found at i:1382707 original size:25 final size:25

Alignment explanation


    Indices: 1382679--1382761  Score: 64
    Period size: 25  Copynumber: 3.2  Consensus size: 25

    1382669 CACATTTCCC

                      *            * 
    1382679 TCTCAATTTTTTTAACTTTTTCTTT
          1 TCTCAATTTTATTAACTTTTTCTCT

                                       
    1382704 TCTC--TTCATTATTAACTTTTTCTCT
          1 TCTCAATT--TTATTAACTTTTTCTCT

                            *           
    1382729 T-TCAATTTTAACTGTTACTTTTTCTCT
          1 TCTCAATTTT-A-T-TAACTTTTTCTCT

                  
    1382756 CTCTCA
          1 -TCTCA

    1382762 CTTCTTCAAC


Statistics
Matches: 46,  Mismatches: 3, Indels: 14
        0.73            0.05        0.22

Matches are distributed among these distances:
  23    2  0.04
  24    4  0.09
  25   21  0.46
  26    3  0.07
  27   12  0.26
  28    1  0.02
  29    3  0.07

ACGTcount: A:0.17, C:0.22, G:0.01, T:0.60


Consensus pattern (25 bp):   
TCTCAATTTTATTAACTTTTTCTCT

Done.