Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001325.1 Hibiscus syriacus cultivar Beakdansim tig00002584_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: 63865
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:1030 original size:15 final size:16

Alignment explanation


    Indices: 1002--1033  Score: 57
    Period size: 15  Copynumber: 2.1  Consensus size: 16

        992 AAAATCTTTC

                            
       1002 TTTCCCGTTCTGGATT
          1 TTTCCCGTTCTGGATT

                            
       1018 TTTCCCG-TCTGGATT
          1 TTTCCCGTTCTGGATT

             
       1033 T
          1 T

       1034 GGATCTGCCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    9  0.56
  16    7  0.44

ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50


Consensus pattern (16 bp):   
TTTCCCGTTCTGGATT

Found at i:1935 original size:12 final size:13

Alignment explanation


    Indices: 1912--1956  Score: 83
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       1902 TAAAAATTAC

                         
       1912 AGCAGCCCCCCTT
          1 AGCAGCCCCCCTT

                         
       1925 AGCAG-CCCCCTT
          1 AGCAGCCCCCCTT

                         
       1937 AGCAGCCCCCCTT
          1 AGCAGCCCCCCTT

                   
       1950 AGCAGCC
          1 AGCAGCC

       1957 ATGTGTTTTA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   12  0.39
  13   19  0.61

ACGTcount: A:0.18, C:0.51, G:0.18, T:0.13


Consensus pattern (13 bp):   
AGCAGCCCCCCTT

Found at i:8034 original size:14 final size:15

Alignment explanation


    Indices: 8006--8034  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       7996 CAGTTGAGAA

                           
       8006 TAAATTAAGGATTTG
          1 TAAATTAAGGATTTG

                           
       8021 TAAATTAA-GATTTG
          1 TAAATTAAGGATTTG

       8035 ACTTTTAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    6  0.43
  15    8  0.57

ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41


Consensus pattern (15 bp):   
TAAATTAAGGATTTG

Found at i:15689 original size:12 final size:12

Alignment explanation


    Indices: 15672--15696  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      15662 TAAAATTTGA

                        
      15672 ACTTCCAATCTT
          1 ACTTCCAATCTT

                        
      15684 ACTTCCAATCTT
          1 ACTTCCAATCTT

             
      15696 A
          1 A

      15697 TTTAAAATAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40


Consensus pattern (12 bp):   
ACTTCCAATCTT

Found at i:16118 original size:2 final size:2

Alignment explanation


    Indices: 16111--16142  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      16101 ATTCTAATCT

                                                           
      16111 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

      16143 ATTTTTCAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:25117 original size:21 final size:23

Alignment explanation


    Indices: 25087--25129  Score: 63
    Period size: 21  Copynumber: 2.0  Consensus size: 23

      25077 TATGAAATTT

                 *                 
      25087 GTCCCGAAGGA-C-CTATGTCCA
          1 GTCCCAAAGGACCACTATGTCCA

                                  
      25108 GTCCCAAAGGACCACTATGTCC
          1 GTCCCAAAGGACCACTATGTCC

      25130 CGAAGGACCT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  21   10  0.53
  22    1  0.05
  23    8  0.42

ACGTcount: A:0.26, C:0.35, G:0.21, T:0.19


Consensus pattern (23 bp):   
GTCCCAAAGGACCACTATGTCCA

Found at i:45225 original size:12 final size:13

Alignment explanation


    Indices: 45208--45247  Score: 50
    Period size: 12  Copynumber: 3.3  Consensus size: 13

      45198 ACATTTATTT

                         
      45208 TTAAAAA-AGTAA
          1 TTAAAAATAGTAA

                         
      45220 TTAAAAATAG-AA
          1 TTAAAAATAGTAA

                     *   
      45232 -TAAAAATAATAA
          1 TTAAAAATAGTAA

                
      45244 TTAA
          1 TTAA

      45248 GATACTAAAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 5
        0.80            0.03        0.17

Matches are distributed among these distances:
  11    8  0.33
  12   11  0.46
  13    5  0.21

ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28


Consensus pattern (13 bp):   
TTAAAAATAGTAA
Done.