Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01000142.1 Hibiscus syriacus cultivar Beakdansim tig00000257_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: 196534
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


File 2 of 2

Found at i:182456 original size:27 final size:26

Alignment explanation


    Indices: 182405--182466  Score: 70
    Period size: 27  Copynumber: 2.3  Consensus size: 26

     182395 TTATTATTAT

                             ** *      
     182405 TATTATAATTATTATTATTATAATATA
          1 TATTATAATTATTATTAAAAAAATA-A

                  *                   
     182432 TATTATTATTATTATTAAAAAAATAA
          1 TATTATAATTATTATTAAAAAAATAA

                     
     182458 TAGTTATAA
          1 TA-TTATAA

     182467 GTCCAAATCC


Statistics
Matches: 29,  Mismatches: 5, Indels: 2
        0.81            0.14        0.06

Matches are distributed among these distances:
  26    3  0.10
  27   26  0.90

ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50


Consensus pattern (26 bp):   
TATTATAATTATTATTAAAAAAATAA

Found at i:182464 original size:24 final size:24

Alignment explanation


    Indices: 182412--182464  Score: 63
    Period size: 24  Copynumber: 2.2  Consensus size: 24

     182402 TATTATTATA

                            * *   * 
     182412 ATTATTATTATTATAATATATATT
          1 ATTATTATTATTATAAAAAATAAT

                                    
     182436 ATTATTATTATTA-AAAAAATAAT
          1 ATTATTATTATTATAAAAAATAAT

                  
     182459 AGTTAT
          1 A-TTAT

     182465 AAGTCCAAAT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  23    8  0.32
  24   17  0.68

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51


Consensus pattern (24 bp):   
ATTATTATTATTATAAAAAATAAT

Found at i:183937 original size:23 final size:26

Alignment explanation


    Indices: 183905--183954  Score: 70
    Period size: 23  Copynumber: 2.0  Consensus size: 26

     183895 CTTTTTCTGA

                 *                    
     183905 TATTTCTAAATA-A-ATAAA-TATTT
          1 TATTTATAAATATATATAAATTATTT

                                      
     183928 TATTTATAAATATATATAAATTATTT
          1 TATTTATAAATATATATAAATTATTT

             
     183954 T
          1 T

     183955 TTAATTATAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  23   11  0.48
  24    1  0.04
  25    5  0.22
  26    6  0.26

ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52


Consensus pattern (26 bp):   
TATTTATAAATATATATAAATTATTT

Found at i:195467 original size:24 final size:25

Alignment explanation


    Indices: 195440--195486  Score: 71
    Period size: 25  Copynumber: 2.0  Consensus size: 25

     195430 TAGCATGTTT

                               *     
     195440 AAAAAT-AAAACTC-AAAATAAAAG
          1 AAAAATGAAAACTCGAAAAGAAAAG

                                    
     195463 AAAAATGAAAACTCGAAAAGAAAA
          1 AAAAATGAAAACTCGAAAAGAAAA

     195487 TAAAGGAGAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  23    6  0.29
  24    7  0.33
  25    8  0.38

ACGTcount: A:0.72, C:0.09, G:0.09, T:0.11


Consensus pattern (25 bp):   
AAAAATGAAAACTCGAAAAGAAAAG

Done.