Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01006573.1 Hibiscus syriacus cultivar Beakdansim tig00016106_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: 1218788
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 7 of 7

Found at i:1193650 original size:20 final size:21

Alignment explanation


    Indices: 1193627--1193669  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 21

    1193617 AGAGTGAATT

                   *       *     
    1193627 CTGGGTTGGTA-GTATCGATA
          1 CTGGGTTAGTAGGTACCGATA

                *                
    1193647 CTGGTTTAGTAGGTACCGATA
          1 CTGGGTTAGTAGGTACCGATA

              
    1193668 CT
          1 CT

    1193670 ACAAGTTAAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  20    9  0.47
  21   10  0.53

ACGTcount: A:0.21, C:0.14, G:0.30, T:0.35


Consensus pattern (21 bp):   
CTGGGTTAGTAGGTACCGATA

Found at i:1193726 original size:21 final size:22

Alignment explanation


    Indices: 1193702--1193755  Score: 67
    Period size: 21  Copynumber: 2.5  Consensus size: 22

    1193692 TATGCATGGG

                            *     
    1193702 ATATCGATACCTAT-ATGAACA
          1 ATATCGATACCTATAACGAACA

                                * 
    1193723 ATATCGATA-CTATAACGAAGA
          1 ATATCGATACCTATAACGAACA

                        
    1193744 AGTATCGATACC
          1 A-TATCGATACC

    1193756 ATTGTGGAGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  20    4  0.14
  21   15  0.54
  22    8  0.29
  23    1  0.04

ACGTcount: A:0.43, C:0.19, G:0.13, T:0.26


Consensus pattern (22 bp):   
ATATCGATACCTATAACGAACA

Found at i:1197809 original size:21 final size:19

Alignment explanation


    Indices: 1197776--1197814  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 19

    1197766 GTGAATTCTA

                         *     
    1197776 GGTTGGTAGTATCTATACT
          1 GGTTGGTAGTATCGATACT

                                
    1197795 GGTTGAGTAGGTATCGATAC
          1 GGTTG-GTA-GTATCGATAC

    1197815 AACAAGGTAA


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

Matches are distributed among these distances:
  19    5  0.29
  20    3  0.18
  21    9  0.53

ACGTcount: A:0.23, C:0.10, G:0.31, T:0.36


Consensus pattern (19 bp):   
GGTTGGTAGTATCGATACT

Found at i:1207978 original size:13 final size:13

Alignment explanation


    Indices: 1207960--1207984  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

    1207950 TCGATCGAAA

                         
    1207960 TGAAAATAAAAAG
          1 TGAAAATAAAAAG

                        
    1207973 TGAAAATAAAAA
          1 TGAAAATAAAAA

    1207985 TAAAAATTTA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16


Consensus pattern (13 bp):   
TGAAAATAAAAAG

Found at i:1211736 original size:24 final size:24

Alignment explanation


    Indices: 1211704--1211758  Score: 110
    Period size: 24  Copynumber: 2.3  Consensus size: 24

    1211694 CAGTGGGGGA

                                    
    1211704 GGTCTCGCTTGATAGCCTTGATTC
          1 GGTCTCGCTTGATAGCCTTGATTC

                                    
    1211728 GGTCTCGCTTGATAGCCTTGATTC
          1 GGTCTCGCTTGATAGCCTTGATTC

                   
    1211752 GGTCTCG
          1 GGTCTCG

    1211759 GGTTCTGAAC


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   31  1.00

ACGTcount: A:0.11, C:0.25, G:0.27, T:0.36


Consensus pattern (24 bp):   
GGTCTCGCTTGATAGCCTTGATTC

Found at i:1216844 original size:18 final size:18

Alignment explanation


    Indices: 1216823--1216858  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

    1216813 TCTTTAGGGG

                              
    1216823 CATAATGGTCCTTCGGGA
          1 CATAATGGTCCTTCGGGA

                *             
    1216841 CATATTGGTCCTTCGGGA
          1 CATAATGGTCCTTCGGGA

    1216859 TAAATTGTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31


Consensus pattern (18 bp):   
CATAATGGTCCTTCGGGA

Found at i:1216865 original size:18 final size:18

Alignment explanation


    Indices: 1216828--1216865  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

    1216818 AGGGGCATAA

                           *  
    1216828 TGGTCCTTCGGGACATAT
          1 TGGTCCTTCGGGACAAAT

                         *    
    1216846 TGGTCCTTCGGGATAAAT
          1 TGGTCCTTCGGGACAAAT

              
    1216864 TG
          1 TG

    1216866 TAAGTGCCCC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.18, C:0.18, G:0.29, T:0.34


Consensus pattern (18 bp):   
TGGTCCTTCGGGACAAAT

Done.