Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01007466.1 Hibiscus syriacus cultivar Beakdansim tig00020485_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: 207968
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 2 of 2

Found at i:197388 original size:23 final size:23

Alignment explanation


    Indices: 197358--197406  Score: 64
    Period size: 23  Copynumber: 2.1  Consensus size: 23

     197348 TGGTTGTTGG

                       *      *     
     197358 TTTAATGG-ATGTTTAGATTTTAT
          1 TTTAATGGTATATTTA-AGTTTAT

                                   
     197381 TTTAATGGTATATTTAAGTTTAT
          1 TTTAATGGTATATTTAAGTTTAT

               
     197404 TTT
          1 TTT

     197407 GGTTCTTTAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  23   17  0.74
  24    6  0.26

ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59


Consensus pattern (23 bp):   
TTTAATGGTATATTTAAGTTTAT

Found at i:199716 original size:21 final size:21

Alignment explanation


    Indices: 199690--199749  Score: 102
    Period size: 21  Copynumber: 2.9  Consensus size: 21

     199680 CAATTAAGAA

                                 
     199690 TCAAGGAGCTTTACTTCATAG
          1 TCAAGGAGCTTTACTTCATAG

                                 
     199711 TCAAGGAGCTTTACTTCATAG
          1 TCAAGGAGCTTTACTTCATAG

                  *  *        
     199732 TCAAGGTGCCTTACTTCA
          1 TCAAGGAGCTTTACTTCA

     199750 AAGCCATATC


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   37  1.00

ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33


Consensus pattern (21 bp):   
TCAAGGAGCTTTACTTCATAG

Found at i:204285 original size:43 final size:40

Alignment explanation


    Indices: 204208--204286  Score: 95
    Period size: 41  Copynumber: 1.9  Consensus size: 40

     204198 TTCTAAATAT

                     *     *   *                    
     204208 TTAACTTTTTCTTTTCTCTTTCATCCTTAATATTTTCTTC
          1 TTAACTTTTACTTTTATCTCTCATCCTTAATATTTTCTTC

                                           *       
     204248 TTAACTTTTACTTTTTATCTCTCATACTCTTCATATTTT
          1 TTAACTTTTAC-TTTTATCTCTCAT-C-CTTAATATTTT

     204287 TCACTCTTTT


Statistics
Matches: 32,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  40   10  0.31
  41   11  0.34
  42    1  0.03
  43   10  0.31

ACGTcount: A:0.18, C:0.22, G:0.00, T:0.61


Consensus pattern (40 bp):   
TTAACTTTTACTTTTATCTCTCATCCTTAATATTTTCTTC

Found at i:206359 original size:23 final size:23

Alignment explanation


    Indices: 206329--206377  Score: 64
    Period size: 23  Copynumber: 2.1  Consensus size: 23

     206319 TGGTGGTTGG

                       *      *     
     206329 TTTAATGG-ATGTTTAGATTTTAT
          1 TTTAATGGTATATTTA-AGTTTAT

                                   
     206352 TTTAATGGTATATTTAAGTTTAT
          1 TTTAATGGTATATTTAAGTTTAT

               
     206375 TTT
          1 TTT

     206378 GGTTCTTTAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  23   17  0.74
  24    6  0.26

ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59


Consensus pattern (23 bp):   
TTTAATGGTATATTTAAGTTTAT

Done.