Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008006.1 Hibiscus syriacus cultivar Beakdansim tig00110468_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: 226016
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


File 2 of 2

Found at i:211487 original size:17 final size:17

Alignment explanation


    Indices: 211454--211487  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

     211444 TTGAATATTT

                     *  *    
     211454 TGGATTGTTTGATTTTG
          1 TGGATTGTTAGACTTTG

                             
     211471 TGGATTGTTAGACTTTG
          1 TGGATTGTTAGACTTTG

     211488 GATTTGTTTG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53


Consensus pattern (17 bp):   
TGGATTGTTAGACTTTG

Found at i:217089 original size:17 final size:17

Alignment explanation


    Indices: 217067--217107  Score: 50
    Period size: 17  Copynumber: 2.5  Consensus size: 17

     217057 TTATCCCATG

                   *          
     217067 TGCACAAGTTGGTC-ACT
          1 TGCACAACTT-GTCAACT

                             
     217084 TGCACAACTTGTCAACT
          1 TGCACAACTTGTCAACT

                    
     217101 TGC-CAAC
          1 TGCACAAC

     217108 CAAGGATGAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  16    7  0.32
  17   15  0.68

ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27


Consensus pattern (17 bp):   
TGCACAACTTGTCAACT

Found at i:217180 original size:43 final size:44

Alignment explanation


    Indices: 217086--217194  Score: 157
    Period size: 43  Copynumber: 2.5  Consensus size: 44

     217076 TGGTCACTTG

                 *   *                                 *
     217086 CACAACTTGTCAACTTGCCAACCAAGGATGAATTATCCCATGTG
          1 CACAAGTTGGCAACTTGCCAACCAAGGATGAATTATCCCATGTA

             *                *                         
     217130 CTCAAGTTGGCAACTTGCTAACCAAGGATGAA-TATCCCATGTA
          1 CACAAGTTGGCAACTTGCCAACCAAGGATGAATTATCCCATGTA

                       *          
     217173 CACAAGTTGGCTACTTGCCAAC
          1 CACAAGTTGGCAACTTGCCAAC

     217195 TGTAAACTTG


Statistics
Matches: 57,  Mismatches: 8, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  43   29  0.51
  44   28  0.49

ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25


Consensus pattern (44 bp):   
CACAAGTTGGCAACTTGCCAACCAAGGATGAATTATCCCATGTA

Found at i:221013 original size:16 final size:16

Alignment explanation


    Indices: 220988--221020  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

     220978 GCCAAACGAT

                            
     220988 TGATTATTCCCCATTC
          1 TGATTATTCCCCATTC

                 *          
     221004 TGATTGTTCCCCATTC
          1 TGATTATTCCCCATTC

             
     221020 T
          1 T

     221021 TTCTCCTCCA


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

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.15, C:0.30, G:0.09, T:0.45


Consensus pattern (16 bp):   
TGATTATTCCCCATTC

Found at i:221847 original size:43 final size:44

Alignment explanation


    Indices: 221760--221858  Score: 137
    Period size: 43  Copynumber: 2.3  Consensus size: 44

     221750 CATAACTTGT

                  *                    *       *        
     221760 CAACTTACCAACCAAGGATAAATTATCTCATGTGCTCAAGTTGG
          1 CAACTTGCCAACCAAGGATAAATTATCCCATGTGCACAAGTTGG

                    *          *                        
     221804 CAACTTGCTAACCAAGGATGAA-TATCCCATGTGCACAAGTTGG
          1 CAACTTGCCAACCAAGGATAAATTATCCCATGTGCACAAGTTGG

             *          
     221847 CTACTTGCCAAC
          1 CAACTTGCCAAC

     221859 TTGTCAACTT


Statistics
Matches: 48,  Mismatches: 7, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  43   29  0.60
  44   19  0.40

ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25


Consensus pattern (44 bp):   
CAACTTGCCAACCAAGGATAAATTATCCCATGTGCACAAGTTGG

Found at i:223718 original size:2 final size:2

Alignment explanation


    Indices: 223711--223775  Score: 130
    Period size: 2  Copynumber: 32.5  Consensus size: 2

     223701 TCGTAAATTT

                                                                          
     223711 TA TA 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 TA TA

                                              
     223753 TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA T

     223776 TGTAGATTGA


Statistics
Matches: 63,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   63  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA


Done.