Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01005037.1 Hibiscus syriacus cultivar Beakdansim tig00011308_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: 65330
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37


Found at i:28107 original size:22 final size:20

Alignment explanation


    Indices: 28082--28121  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      28072 TCACATATTT

                                  
      28082 ATTTTAAACTTTGATATAAAGG
          1 ATTTTAAA-TTT-ATATAAAGG

                  *           
      28104 ATTTTATATTTATATAAA
          1 ATTTTAAATTTATATAAA

      28122 TTTATTATAG


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

Matches are distributed among these distances:
  20    7  0.41
  21    3  0.18
  22    7  0.41

ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47


Consensus pattern (20 bp):   
ATTTTAAATTTATATAAAGG

Found at i:30161 original size:22 final size:20

Alignment explanation


    Indices: 30136--30176  Score: 55
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      30126 TCACATATTT

                                  
      30136 ATTTTAAACTTTGATATAAATG
          1 ATTTTAAA-TTT-ATATAAATG

                  *            
      30158 ATTTTATATTTATATAAAT
          1 ATTTTAAATTTATATAAAT

      30177 TTATTATACG


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    8  0.44
  21    3  0.17
  22    7  0.39

ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51


Consensus pattern (20 bp):   
ATTTTAAATTTATATAAATG

Found at i:49241 original size:15 final size:15

Alignment explanation


    Indices: 49221--49257  Score: 51
    Period size: 14  Copynumber: 2.5  Consensus size: 15

      49211 CCGAAATATA

                            
      49221 GAAATCAGATATT-AG
          1 GAAATCA-ATATTCAG

                           
      49236 GAAATCAATATTCAG
          1 GAAATCAATATTCAG

                    
      49251 G-AATCAA
          1 GAAATCAA

      49258 GTATCATGTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  14   11  0.52
  15   10  0.48

ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24


Consensus pattern (15 bp):   
GAAATCAATATTCAG

Found at i:50232 original size:23 final size:23

Alignment explanation


    Indices: 50205--50251  Score: 76
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      50195 CAACGGTCAA

                      *   *        
      50205 CGGGTCGGGTTAACGGGTCGGGT
          1 CGGGTCGGGTCAACAGGTCGGGT

                                   
      50228 CGGGTCGGGTCAACAGGTCGGGT
          1 CGGGTCGGGTCAACAGGTCGGGT

             
      50251 C
          1 C

      50252 AAAACCAATC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.11, C:0.21, G:0.49, T:0.19


Consensus pattern (23 bp):   
CGGGTCGGGTCAACAGGTCGGGT

Found at i:50251 original size:13 final size:13

Alignment explanation


    Indices: 50199--50253  Score: 71
    Period size: 13  Copynumber: 4.5  Consensus size: 13

      50189 CCCTATCAAC

                         
      50199 GGTCAACGGGTCG
          1 GGTCAACGGGTCG

               *         
      50212 GGTTAACGGGTCG
          1 GGTCAACGGGTCG

                         
      50225 GGT---CGGGTCG
          1 GGTCAACGGGTCG

                   *     
      50235 GGTCAACAGGTCG
          1 GGTCAACGGGTCG

                  
      50248 GGTCAA
          1 GGTCAA

      50254 AACCAATCAA


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

Matches are distributed among these distances:
  10   10  0.27
  13   27  0.73

ACGTcount: A:0.16, C:0.20, G:0.45, T:0.18


Consensus pattern (13 bp):   
GGTCAACGGGTCG

Found at i:56472 original size:15 final size:15

Alignment explanation


    Indices: 56452--56488  Score: 51
    Period size: 15  Copynumber: 2.5  Consensus size: 15

      56442 CCGAAATACA

                            
      56452 GAAATCAGATA-TCAG
          1 GAAATCA-ATATTCAG

                           
      56467 GAAATCAATATTCAG
          1 GAAATCAATATTCAG

                    
      56482 G-AATCAA
          1 GAAATCAA

      56489 GTGTCATGTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  14    9  0.43
  15   12  0.57

ACGTcount: A:0.49, C:0.14, G:0.16, T:0.22


Consensus pattern (15 bp):   
GAAATCAATATTCAG

Found at i:57328 original size:25 final size:25

Alignment explanation


    Indices: 57307--57360  Score: 72
    Period size: 27  Copynumber: 2.1  Consensus size: 25

      57297 ACTAAAATGT

                    *                
      57307 CATTTTTTCAAAATTACGAAAATAA
          1 CATTTTTTAAAAATTACGAAAATAA

                               *       
      57332 CATTTTTTAAAAAAATTACAAAAATAA
          1 CATTTTTT--AAAAATTACGAAAATAA

              
      57359 CA
          1 CA

      57361 CCCTTTTCGA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  25    8  0.32
  27   17  0.68

ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33


Consensus pattern (25 bp):   
CATTTTTTAAAAATTACGAAAATAA
Done.