Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01002322.1 Hibiscus syriacus cultivar Beakdansim tig00004732_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: 168257
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


File 2 of 2

Found at i:155745 original size:15 final size:16

Alignment explanation


    Indices: 155717--155750  Score: 52
    Period size: 15  Copynumber: 2.2  Consensus size: 16

     155707 CAAATCTTAC

                            
     155717 TTTATAAAATAATATA
          1 TTTATAAAATAATATA

                   *        
     155733 TTTATAATA-AATATA
          1 TTTATAAAATAATATA

               
     155748 TTT
          1 TTT

     155751 TTTTAATTAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    9  0.53
  16    8  0.47

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


Consensus pattern (16 bp):   
TTTATAAAATAATATA

Found at i:158290 original size:42 final size:42

Alignment explanation


    Indices: 158198--158314  Score: 146
    Period size: 42  Copynumber: 2.8  Consensus size: 42

     158188 GTAATCCAAG

                                  * *                  
     158198 CCGAAATTCAAAACCATCGAAATCTTTCTAACATATGCCTAAT
          1 CCGAAATTCAAAACCATC-AAACCGTTCTAACATATGCCTAAT

                                           *    *     
     158241 CCG-AATTCAAAACCATCAAACCGTTCTAACGTATGGCTAAT
          1 CCGAAATTCAAAACCATCAAACCGTTCTAACATATGCCTAAT

                     *    *   *              
     158282 CCGAAATTCGAAACTATAGAAACCGTTCTAACA
          1 CCGAAATTCAAAACCAT-CAAACCGTTCTAACA

     158315 GAAACCAATT


Statistics
Matches: 64,  Mismatches: 8, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  41   23  0.36
  42   25  0.39
  43   16  0.25

ACGTcount: A:0.39, C:0.26, G:0.10, T:0.25


Consensus pattern (42 bp):   
CCGAAATTCAAAACCATCAAACCGTTCTAACATATGCCTAAT

Found at i:159192 original size:35 final size:34

Alignment explanation


    Indices: 159153--159230  Score: 95
    Period size: 35  Copynumber: 2.2  Consensus size: 34

     159143 ATTCCTTAAT

                                      *         
     159153 TTCATTCTAAACTCC-AAATTCCAAAGTAATTCAAA
          1 TTCATTCTAAAC-CCTAAATTCCAAAATAATTC-AA

                  *              *            
     159188 TTCATTATAAACCCTAAATTCTAAAATAATTCAA
          1 TTCATTCTAAACCCTAAATTCCAAAATAATTCAA

                     
     159222 TTACATTCT
          1 TT-CATTCT

     159231 CCCAAATTCT


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  34    6  0.16
  35   31  0.84

ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36


Consensus pattern (34 bp):   
TTCATTCTAAACCCTAAATTCCAAAATAATTCAA

Found at i:160336 original size:35 final size:35

Alignment explanation


    Indices: 160287--160399  Score: 147
    Period size: 35  Copynumber: 3.2  Consensus size: 35

     160277 AAAAAAGACA

                     *      *                 *
     160287 GAAATTGAAGTATTTTAGAATTTGAGTTTTAGAAC
          1 GAAATTGAATTATTTTGGAATTTGAGTTTTAGAAT

             *                                  
     160322 GTAATTGAATTATTTTGGAATTT-AGTGTTTAGAAT
          1 GAAATTGAATTATTTTGGAATTTGAGT-TTTAGAAT

                        *           * *        
     160357 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
          1 GAAATTGAATTATTTTGGAATTTGAGTTTTAGAAT

                    
     160392 GAAATTGA
          1 GAAATTGA

     160400 TGATTGTTTT


Statistics
Matches: 68,  Mismatches: 8, Indels: 4
        0.85            0.10        0.05

Matches are distributed among these distances:
  34    3  0.04
  35   64  0.94
  36    1  0.01

ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42


Consensus pattern (35 bp):   
GAAATTGAATTATTTTGGAATTTGAGTTTTAGAAT

Done.