Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01007949.1 Hibiscus syriacus cultivar Beakdansim tig00110371_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: 222664
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


File 2 of 2

Found at i:217976 original size:27 final size:29

Alignment explanation


    Indices: 217945--218009  Score: 71
    Period size: 30  Copynumber: 2.3  Consensus size: 29

     217935 TCTTGAGACA

                     *                   
     217945 ATTTCTTTTGA-AAAA-ATCTTTGAGTCT
          1 ATTTCTTTTAACAAAACATCTTTGAGTCT

            *     *                     * 
     217972 GTTTCTCTTAACAAAATCATCTTTGAGTTT
          1 ATTTCTTTTAACAAAA-CATCTTTGAGTCT

                    
     218002 ATTTCTTT
          1 ATTTCTTT

     218010 AAAAACAAAT


Statistics
Matches: 29,  Mismatches: 6, Indels: 3
        0.76            0.16        0.08

Matches are distributed among these distances:
  27    8  0.28
  28    4  0.14
  30   17  0.59

ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51


Consensus pattern (29 bp):   
ATTTCTTTTAACAAAACATCTTTGAGTCT

Found at i:218157 original size:120 final size:119

Alignment explanation


    Indices: 217989--218211  Score: 258
    Period size: 120  Copynumber: 1.9  Consensus size: 119

     217979 TTAACAAAAT

                  *    *                        *      *     *               
     217989 CATCTTTGAGTTTATTTCTTTAAAAACAAATGTTGTCTCTCTTGAGACAGTTTCTAATT-AAAAA
          1 CATCTTCGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCT-ATTGAAAAA

                                                                      
     218053 CTAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTTACTTAAGATGTAATC
         65 --AATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTTACTTAAGATGTAATC

                                 **                                  *       
     218109 CATCTTCGAGTCTATTTCTTTTGAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTTTTGAAAA
          1 CATCTTCGAGTCTATTTCTTTAAAAAC-AAATGTTGTATCTCTT-AAGACAATTTCTATTGAAAA

                       *       *               *    
     218172 AAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCT
         64 AAATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCT

     218212 CTCGAGACAA


Statistics
Matches: 87,  Mismatches: 11, Indels: 11
        0.80            0.10        0.10

Matches are distributed among these distances:
 118   23  0.26
 119   20  0.23
 120   40  0.46
 121    4  0.05

ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43


Consensus pattern (119 bp):   
CATCTTCGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTATTGAAAAAA
ATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTTACTTAAGATGTAATC

Found at i:218291 original size:38 final size:40

Alignment explanation


    Indices: 218216--218293  Score: 133
    Period size: 38  Copynumber: 2.0  Consensus size: 40

     218206 TTGTCTCTCG

                                                    
     218216 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT
          1 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT

                                            *       
     218256 AGACAACTTCTTTTG-AAATA-CCACCTTTGATATCGTTT
          1 AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT

     218294 CTATTAAAAC


Statistics
Matches: 37,  Mismatches: 1, Indels: 2
        0.93            0.03        0.05

Matches are distributed among these distances:
  38   17  0.46
  39    5  0.14
  40   15  0.41

ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37


Consensus pattern (40 bp):   
AGACAACTTCTTTTGAAAATACCCACCTTTGAGATCGTTT

Found at i:218569 original size:1 final size:1

Alignment explanation


    Indices: 218563--218590  Score: 56
    Period size: 1  Copynumber: 28.0  Consensus size: 1

     218553 ATGTCTTTTC

                                        
     218563 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA

     218591 TTGAAACTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   27  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:219207 original size:40 final size:40

Alignment explanation


    Indices: 219152--219259  Score: 182
    Period size: 40  Copynumber: 2.7  Consensus size: 40

     219142 AGATGGCCAG

                                                     
     219152 AACTCTTCATCACGTATGAGCCGTGTCA-TCCCCGGACCAA
          1 AACTCTTCATCACGTATGAGCCGTGTCATTCCCC-GACCAA

                                                   *
     219192 AACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAG
          1 AACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAA

             *                          
     219232 ATCTCTTCATCACGTATGAGCCGTGTCA
          1 AACTCTTCATCACGTATGAGCCGTGTCA

     219260 CCCTAGATAA


Statistics
Matches: 65,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  40   60  0.92
  41    5  0.08

ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26


Consensus pattern (40 bp):   
AACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAA

Found at i:219596 original size:3 final size:3

Alignment explanation


    Indices: 219590--219636  Score: 60
    Period size: 3  Copynumber: 16.0  Consensus size: 3

     219580 TTTCCGTTAT

                                             **                     *      
     219590 TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA TT- TTA TTA TTA ATA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

     219637 CATTTACATA


Statistics
Matches: 37,  Mismatches: 6, Indels: 2
        0.82            0.13        0.04

Matches are distributed among these distances:
   2    2  0.05
   3   35  0.95

ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64


Consensus pattern (3 bp):   
TTA


Done.