Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008437.1 Hibiscus syriacus cultivar Beakdansim tig00111236_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: 223559
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 2 of 2

Found at i:208585 original size:39 final size:36

Alignment explanation


    Indices: 208477--208633  Score: 105
    Period size: 39  Copynumber: 4.3  Consensus size: 36

     208467 ACATACCAAT

                  *                               
     208477 ATATAAAATA-TA-AATATAATATATAAATACATATAA
          1 ATATAATATACTATAATATAATATATAAAT--ATATAA

                 *                                  
     208513 ATATACTATACTATAATAATAATA-ATAATAATATACTAA
          1 ATATAATATACTATAAT-ATAATATAT-A-AATATA-TAA

                      *                 *        
     208552 ATATAATATATTACTAATATAATATATACA-ATAT--
          1 ATATAATATACTA-TAATATAATATATAAATATATAA

             *                            *       
     208586 AGAT-ATATACTATAATATATGATATATAACTA-ATAA
          1 ATATAATATACTATAATATA--ATATATAAATATATAA

                        
     208622 TATATATATATA
          1 -ATATA-ATATA

     208634 TTAAATTTGT


Statistics
Matches: 95,  Mismatches: 10, Indels: 29
        0.71            0.07        0.22

Matches are distributed among these distances:
  32    7  0.07
  33    7  0.07
  34   12  0.13
  35    1  0.01
  36    9  0.09
  37    8  0.08
  38    9  0.09
  39   33  0.35
  40    9  0.09

ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38


Consensus pattern (36 bp):   
ATATAATATACTATAATATAATATATAAATATATAA

Found at i:208956 original size:2 final size:2

Alignment explanation


    Indices: 208951--208975  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

     208941 TTCTTTTTGA

                                                 
     208951 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

     208976 CACATAATAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:220356 original size:2 final size:2

Alignment explanation


    Indices: 220349--220383  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

     220339 TCAAGTTTTC

                                                                
     220349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

     220384 CATAATTTTC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:223165 original size:35 final size:33

Alignment explanation


    Indices: 223126--223191  Score: 87
    Period size: 35  Copynumber: 1.9  Consensus size: 33

     223116 AATTATATAT

                                       *       
     223126 TTATTTTATTTATTTATTATGTTTTCATAATTTAA
          1 TTATTTTATTTATTTATT-T-TTTTCAAAATTTAA

                   *   *                   
     223161 TTATTTTGTTTGTTTATTTTTTTCAAAATTT
          1 TTATTTTATTTATTTATTTTTTTCAAAATTT

     223192 TGATGCCAAT


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  33   11  0.39
  34    1  0.04
  35   16  0.57

ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68


Consensus pattern (33 bp):   
TTATTTTATTTATTTATTTTTTTCAAAATTTAA

Done.