Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01000796.1 Hibiscus syriacus cultivar Beakdansim tig00001541_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: 52044
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33


Found at i:18503 original size:29 final size:29

Alignment explanation


    Indices: 18460--18542  Score: 139
    Period size: 29  Copynumber: 2.8  Consensus size: 29

      18450 CTCACCTAAC

                                          
      18460 TAAATTGATGTAAGCAATGACATCATTAAT
          1 TAAA-TGATGTAAGCAATGACATCATTAAT

                                   *     
      18490 TAAATGATGTAAGCAATGACATCTTTAAT
          1 TAAATGATGTAAGCAATGACATCATTAAT

                         *          
      18519 TAAATGATGTAAGTAATGACATCA
          1 TAAATGATGTAAGCAATGACATCA

      18543 ATTTAGTTTG


Statistics
Matches: 50,  Mismatches: 3, Indels: 1
        0.93            0.06        0.02

Matches are distributed among these distances:
  29   46  0.92
  30    4  0.08

ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33


Consensus pattern (29 bp):   
TAAATGATGTAAGCAATGACATCATTAAT

Found at i:23267 original size:29 final size:29

Alignment explanation


    Indices: 23224--23306  Score: 139
    Period size: 29  Copynumber: 2.8  Consensus size: 29

      23214 CTCACCTAAC

                                          
      23224 TAAATTGATGTAAGCAATGACATCATTAAT
          1 TAAA-TGATGTAAGCAATGACATCATTAAT

                                   *     
      23254 TAAATGATGTAAGCAATGACATCTTTAAT
          1 TAAATGATGTAAGCAATGACATCATTAAT

                         *          
      23283 TAAATGATGTAAGTAATGACATCA
          1 TAAATGATGTAAGCAATGACATCA

      23307 ATTTAGTTTG


Statistics
Matches: 50,  Mismatches: 3, Indels: 1
        0.93            0.06        0.02

Matches are distributed among these distances:
  29   46  0.92
  30    4  0.08

ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33


Consensus pattern (29 bp):   
TAAATGATGTAAGCAATGACATCATTAAT

Found at i:40203 original size:31 final size:29

Alignment explanation


    Indices: 40150--40208  Score: 73
    Period size: 31  Copynumber: 2.0  Consensus size: 29

      40140 AATATAATTT

                    *              *     
      40150 TAAAAAAATATAAAACTTAGATATTAAAA
          1 TAAAAAAAAATAAAACTTAGATACTAAAA

                             *            
      40179 TAAAAGAAAAATAATAATTTAGATACTAAA
          1 TAAAA-AAAAATAA-AACTTAGATACTAAA

      40209 CATATAATTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  29    5  0.20
  30    7  0.28
  31   13  0.52

ACGTcount: A:0.64, C:0.03, G:0.05, T:0.27


Consensus pattern (29 bp):   
TAAAAAAAAATAAAACTTAGATACTAAAA

Found at i:42259 original size:2 final size:2

Alignment explanation


    Indices: 42252--42289  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      42242 GAGACCTCAC

                                                                    
      42252 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      42290 CCCTTTTTGT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:43132 original size:30 final size:30

Alignment explanation


    Indices: 43072--43133  Score: 72
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      43062 TATATCGCAG

                   *             *  **    
      43072 CAACGCCTCAGCCCCAGCACCGCATCGCCC
          1 CAACGCCCCAGCCCCAGCACCCCAAAGCCC

                                           
      43102 CAACGCCCCAGCCCCAG-ACCCCCAAAGCCC
          1 CAACGCCCCAGCCCCAGCA-CCCCAAAGCCC

              
      43132 CA
          1 CA

      43134 GATAAACAGC


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  29    1  0.04
  30   26  0.96

ACGTcount: A:0.24, C:0.58, G:0.15, T:0.03


Consensus pattern (30 bp):   
CAACGCCCCAGCCCCAGCACCCCAAAGCCC
Done.