Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001581.1 Hibiscus syriacus cultivar Beakdansim tig00003147_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: 220942
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


File 2 of 2

Found at i:210193 original size:24 final size:25

Alignment explanation


    Indices: 210138--210194  Score: 73
    Period size: 24  Copynumber: 2.3  Consensus size: 25

     210128 AATTTGAAAC

                                     
     210138 AATTATAATATATTAATATATATAA
          1 AATTATAATATATTAATATATATAA

              *                        
     210163 ACTTTATAATA-A-TAATATATATATA
          1 A-ATTATAATATATTAATATATATA-A

                   
     210188 AATTATA
          1 AATTATA

     210195 TAGTTTATAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 5
        0.80            0.06        0.14

Matches are distributed among these distances:
  24   16  0.57
  25    4  0.14
  26    8  0.29

ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44


Consensus pattern (25 bp):   
AATTATAATATATTAATATATATAA

Found at i:210395 original size:3 final size:3

Alignment explanation


    Indices: 210387--210446  Score: 57
    Period size: 3  Copynumber: 19.3  Consensus size: 3

     210377 GATGTTTTTA

                          *   *   *   *                  *               
     210387 TAT TAT TAT TAG TAA TAG TAG TAT TAT TAAT TAT AAT TATT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA-T TAT TAT

                             
     210434 TAT TAT TAT TAT T
          1 TAT TAT TAT TAT T

     210447 TCAAGCTTTA


Statistics
Matches: 49,  Mismatches: 6, Indels: 4
        0.83            0.10        0.07

Matches are distributed among these distances:
   3   43  0.88
   4    6  0.12

ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58


Consensus pattern (3 bp):   
TAT

Found at i:212836 original size:130 final size:130

Alignment explanation


    Indices: 212622--212981  Score: 456
    Period size: 130  Copynumber: 2.8  Consensus size: 130

     212612 GAGAATAGTA

                                             * *                             
     212622 ATATATCTTCATTTCGATTGGAGTAATAAATGATTACTTTAAGGAATGAGAGGTC-TTGTATTCT
          1 ATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGAATGAGAGGTCATT-TATTCT

                                   *           *   *        *          *     
     212686 CGATTGGAAATAATTTGATATTACCATTTTCTCTCGAATTAATATTGATTTTTAAGACGGAATAA
         65 CGA-TGGAAATAATTTGATATTATCATTTTCTCTCAAATCAATATTGAGTTTTAAGACGAAATAA

              
     212751 TG
        129 TG

                                *                       *                    
     212753 ATATATCTTCATTTCGATT-AAGTAATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTC
          1 ATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGAATGAGAGGTCATTTATTCTC

                 *    *   *               *        *                *      * 
     212817 GATCGAAAATCATTAGATATTATCATTTTCACTCAAATCGATATTGAGTTTTAAGATGAAATAGT
         66 GAT-GGAAATAATTTGATATTATCATTTTCTCTCAAATCAATATTGAGTTTTAAGACGAAATAAT

             
     212882 G
        130 G

                      *    *                       *     **       *          
     212883 ATAT-TCCTTAATTTTGATTGGAGTAATAAATGACTGCTCTAAGGCGTGAGAGGCCATTTATTCT
          1 ATATAT-CTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGAATGAGAGGTCATTTATTCT

                                               
     212947 CGAGTGGAAATAATTTGATATTATCATTTTCTCTC
         65 CGA-TGGAAATAATTTGATATTATCATTTTCTCTC

     212982 TTAAAATTAT


Statistics
Matches: 197,  Mismatches: 27, Indels: 10
        0.84            0.12        0.04

Matches are distributed among these distances:
 129    2  0.01
 130  105  0.53
 131   89  0.45
 132    1  0.01

ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39


Consensus pattern (130 bp):   
ATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGAATGAGAGGTCATTTATTCTC
GATGGAAATAATTTGATATTATCATTTTCTCTCAAATCAATATTGAGTTTTAAGACGAAATAATG


Done.