Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01006195.1 Hibiscus syriacus cultivar Beakdansim tig00014744_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: 201095
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


File 2 of 2

Found at i:186706 original size:24 final size:23

Alignment explanation


    Indices: 186645--186706  Score: 54
    Period size: 24  Copynumber: 2.6  Consensus size: 23

     186635 AAATTCTAAT

                                    
     186645 CTAATTTGAATTTACTTTTTATTA
          1 CTAATTT-AATTTACTTTTTATTA

            *      * *               
     186669 TTAATTGCATTTTA-TCTTTTATTA
          1 CTAATT-TAATTTACT-TTTTATTA

                          
     186693 CTAATTATAATTTA
          1 CTAATT-TAATTTA

     186707 ATAAGAATTT


Statistics
Matches: 29,  Mismatches: 7, Indels: 4
        0.73            0.17        0.10

Matches are distributed among these distances:
  23    1  0.03
  24   28  0.97

ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58


Consensus pattern (23 bp):   
CTAATTTAATTTACTTTTTATTA

Found at i:197033 original size:6 final size:6

Alignment explanation


    Indices: 197022--197054  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

     197012 GACACGTATT

                                     *            
     197022 ACCACG ACCACG ACCACG ACCATG ACCACG ACC
          1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC

     197055 CGAGTCGAGA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.33, C:0.48, G:0.15, T:0.03


Consensus pattern (6 bp):   
ACCACG

Found at i:198130 original size:16 final size:17

Alignment explanation


    Indices: 198040--198136  Score: 64
    Period size: 17  Copynumber: 5.9  Consensus size: 17

     198030 TTTTTAATCT

                             
     198040 TTTATTT-TTATT-TT-
          1 TTTATTTATTATTATTG

                   *         
     198054 TTTATTTTTTA-TA-TG
          1 TTTATTTATTATTATTG

             *                *
     198069 TATATATTATTATTATATA
          1 TTTAT-TTATTATTAT-TG

             *        *   *   
     198088 TATATTT-TCCATTCTTG
          1 TTTATTTAT-TATTATTG

                             
     198105 TTTATTTATTATTATTG
          1 TTTATTTATTATTATTG

                            
     198122 TTT-TTTATTATTATT
          1 TTTATTTATTATTATT

     198137 TTAATCTACA


Statistics
Matches: 65,  Mismatches: 9, Indels: 16
        0.72            0.10        0.18

Matches are distributed among these distances:
  14    9  0.14
  15    7  0.11
  16   17  0.26
  17   19  0.29
  18    7  0.11
  19    6  0.09

ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70


Consensus pattern (17 bp):   
TTTATTTATTATTATTG

Found at i:198153 original size:2 final size:2

Alignment explanation


    Indices: 198146--198171  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

     198136 TTTAATCTAC

                                                  
     198146 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

     198172 TTTGCATCTC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:198411 original size:23 final size:24

Alignment explanation


    Indices: 198385--198442  Score: 59
    Period size: 24  Copynumber: 2.5  Consensus size: 24

     198375 TGTATATAGA

                                     
     198385 TTATTACTTTTTTATTTGT-TA-TT
          1 TTATT-CTTTTTTATTTGTGTATTT

                             *       
     198408 TTATT-TTATTTTATTTTTGTATTT
          1 TTATTCTT-TTTTATTTGTGTATTT

                  *    
     198432 TTATTCCTTTT
          1 TTATTCTTTTT

     198443 CTCTTTATCT


Statistics
Matches: 29,  Mismatches: 2, Indels: 7
        0.76            0.05        0.18

Matches are distributed among these distances:
  21    2  0.07
  22    9  0.31
  23    7  0.24
  24   10  0.34
  25    1  0.03

ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76


Consensus pattern (24 bp):   
TTATTCTTTTTTATTTGTGTATTT

Done.