Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001042.1 Hibiscus syriacus cultivar Beakdansim tig00002070_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: 47072
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:5489 original size:13 final size:13

Alignment explanation


    Indices: 5471--5497  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       5461 GGTACTGAAA

                         
       5471 CGATGTGAGGAAG
          1 CGATGTGAGGAAG

                         
       5484 CGATGTGAGGAAG
          1 CGATGTGAGGAAG

             
       5497 C
          1 C

       5498 TGATCTCTTG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.30, C:0.11, G:0.44, T:0.15


Consensus pattern (13 bp):   
CGATGTGAGGAAG

Found at i:9103 original size:18 final size:18

Alignment explanation


    Indices: 9080--9114  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       9070 TTTCTAGCTG

                              
       9080 CCCATGTTGGACCACTGC
          1 CCCATGTTGGACCACTGC

                        *    
       9098 CCCATGTTGGACTACTG
          1 CCCATGTTGGACCACTG

       9115 TCCAATCCTC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.17, C:0.34, G:0.23, T:0.26


Consensus pattern (18 bp):   
CCCATGTTGGACCACTGC

Found at i:18515 original size:20 final size:19

Alignment explanation


    Indices: 18469--18517  Score: 55
    Period size: 20  Copynumber: 2.6  Consensus size: 19

      18459 AGAACTTTTC

                             * 
      18469 CAAATTCATA-ATTTATTT
          1 CAAATTCATAGATTTATAT

              *        *        
      18487 CAGATTCATAGTTTTACTAT
          1 CAAATTCATAGATTTA-TAT

                       
      18507 CAAATTCATAG
          1 CAAATTCATAG

      18518 CCTAATGTAT


Statistics
Matches: 25,  Mismatches: 4, Indels: 2
        0.81            0.13        0.06

Matches are distributed among these distances:
  18    9  0.36
  19    4  0.16
  20   12  0.48

ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43


Consensus pattern (19 bp):   
CAAATTCATAGATTTATAT

Found at i:21963 original size:39 final size:39

Alignment explanation


    Indices: 21907--22006  Score: 112
    Period size: 39  Copynumber: 2.5  Consensus size: 39

      21897 GAAATGAAGA

                     *                               
      21907 GAAAAATGGTGAATTAGGGATTG-AGATACGAAAGAGAAAT
          1 GAAAAA-GGGGAATTAGGGATTGAAG-TACGAAAGAGAAAT

                                      **  *  *   * 
      21947 GAAAAAGGGGAATTAGGGATTGAAGTGTGAGAGGGAATT
          1 GAAAAAGGGGAATTAGGGATTGAAGTACGAAAGAGAAAT

                 *               
      21986 GAAAATGGGGAATTAGGGATT
          1 GAAAAAGGGGAATTAGGGATT

      22007 CTGGAAATTG


Statistics
Matches: 52,  Mismatches: 7, Indels: 3
        0.84            0.11        0.05

Matches are distributed among these distances:
  39   44  0.85
  40    8  0.15

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


Consensus pattern (39 bp):   
GAAAAAGGGGAATTAGGGATTGAAGTACGAAAGAGAAAT

Found at i:27038 original size:39 final size:39

Alignment explanation


    Indices: 26993--27082  Score: 132
    Period size: 39  Copynumber: 2.3  Consensus size: 39

      26983 GGAAAATTAT

                                                      
      26993 GAATTAGGGATTG-AGATGCG-AAGGAGAAATGAAAAA-GGG
          1 GAATTAGGGATTGAAG-TGCGAAAGG-GAAAT-AAAAATGGG

                                                   
      27032 GAATTAGGGATTGAAGTGCGAAAGGGAAATAAAAATGGG
          1 GAATTAGGGATTGAAGTGCGAAAGGGAAATAAAAATGGG

                        
      27071 GAATTAGGGATT
          1 GAATTAGGGATT

      27083 CTGGAAATTG


Statistics
Matches: 48,  Mismatches: 0, Indels: 6
        0.89            0.00        0.11

Matches are distributed among these distances:
  38    5  0.10
  39   37  0.77
  40    6  0.12

ACGTcount: A:0.42, C:0.02, G:0.37, T:0.19


Consensus pattern (39 bp):   
GAATTAGGGATTGAAGTGCGAAAGGGAAATAAAAATGGG

Found at i:30062 original size:29 final size:30

Alignment explanation


    Indices: 30008--30064  Score: 89
    Period size: 29  Copynumber: 1.9  Consensus size: 30

      29998 TGTTAGTGTT

                                 *        
      30008 CGTTTGTTTATTTTTAAAGGTGTTTATGTC
          1 CGTTTGTTTATTTTTAAAGGTATTTATGTC

                             *          
      30038 CGTTTG-TTATTTTTAACGGTATTTATG
          1 CGTTTGTTTATTTTTAAAGGTATTTATG

      30065 CATGCTTGGT


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  29   19  0.76
  30    6  0.24

ACGTcount: A:0.18, C:0.07, G:0.19, T:0.56


Consensus pattern (30 bp):   
CGTTTGTTTATTTTTAAAGGTATTTATGTC

Found at i:46559 original size:20 final size:21

Alignment explanation


    Indices: 46526--46565  Score: 64
    Period size: 20  Copynumber: 1.9  Consensus size: 21

      46516 TGTTTCATGT

                                  
      46526 ATATATAGAAAGAGAGAGGGAG
          1 ATATATAG-AAGAGAGAGGGAG

                               
      46548 ATATATAG-AGAGAGAGGG
          1 ATATATAGAAGAGAGAGGG

      46566 GGGAGAGTGA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20   10  0.56
  22    8  0.44

ACGTcount: A:0.47, C:0.00, G:0.38, T:0.15


Consensus pattern (21 bp):   
ATATATAGAAGAGAGAGGGAG
Done.