Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01009469.1 Hibiscus syriacus cultivar Beakdansim tig00114139_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: 23809
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38


Found at i:1058 original size:28 final size:27

Alignment explanation


    Indices: 991--1058  Score: 75
    Period size: 28  Copynumber: 2.4  Consensus size: 27

        981 CTCATAATTC

                              *         
        991 TAATAATATGATATATATTCTTTAATAT
          1 TAATAATAT-ATATATATACTTTAATAT

                                    *  * 
       1019 T-ATAATGATATATATTATACTTTTATTT
          1 TAATAAT-ATATATA-TATACTTTAATAT

                        
       1047 TAATAATATATA
          1 TAATAATATATA

       1059 ATGATTTTTT


Statistics
Matches: 34,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
  27   10  0.29
  28   19  0.56
  29    5  0.15

ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51


Consensus pattern (27 bp):   
TAATAATATATATATATACTTTAATAT

Found at i:3611 original size:29 final size:30

Alignment explanation


    Indices: 3574--3642  Score: 72
    Period size: 29  Copynumber: 2.3  Consensus size: 30

       3564 CTCATAATTC

                              *            
       3574 TAATAATATGAATA-TATTCTTTAATATT-A
          1 TAAT-ATATGAATATTATACTTTAATATTAA

                                   *  *    
       3603 TAATGATAT-AATATTATACTTTTATTTTAA
          1 TAAT-ATATGAATATTATACTTTAATATTAA

                      
       3633 TAATATATGA
          1 TAATATATGA

       3643 TTTTTCAATA


Statistics
Matches: 33,  Mismatches: 4, Indels: 5
        0.79            0.10        0.12

Matches are distributed among these distances:
  28    4  0.12
  29   23  0.70
  30    6  0.18

ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49


Consensus pattern (30 bp):   
TAATATATGAATATTATACTTTAATATTAA

Found at i:5401 original size:11 final size:11

Alignment explanation


    Indices: 5385--5414  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

       5375 ATTTTATACT

                       
       5385 ATTTTAATAAC
          1 ATTTTAATAAC

                       
       5396 ATTTTAATAAC
          1 ATTTTAATAAC

               *    
       5407 ATTATAAT
          1 ATTTTAAT

       5415 GATATATAAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47


Consensus pattern (11 bp):   
ATTTTAATAAC

Found at i:5429 original size:61 final size:65

Alignment explanation


    Indices: 5310--5441  Score: 191
    Period size: 68  Copynumber: 2.0  Consensus size: 65

       5300 CAAAACCTTA

                                                          *                  
       5310 TTATACTATTTTAATAACATTTTAATAAAAAATTAAAATAATGATTTTAATAATATTATACTTTT
          1 TTATACTATTTTAATAACATTTTAAT-AAAAATT--AATAATGATTATAATAATATTATACTTTT

               
       5375 ATT
         63 ATT

                                         *                                   
       5378 TTATACTATTTTAATAACATTTTAAT-AACATT-ATAATGA-TAT-ATAATATTATACTTTTATT
          1 TTATACTATTTTAATAACATTTTAATAAAAATTAATAATGATTATAATAATATTATACTTTTATT

               
       5439 TTA
          1 TTA

       5442 ATAATATATA


Statistics
Matches: 62,  Mismatches: 2, Indels: 7
        0.87            0.03        0.10

Matches are distributed among these distances:
  61   22  0.35
  62    2  0.03
  63    7  0.11
  66    5  0.08
  68   26  0.42

ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50


Consensus pattern (65 bp):   
TTATACTATTTTAATAACATTTTAATAAAAATTAATAATGATTATAATAATATTATACTTTTATT

Found at i:13644 original size:18 final size:19

Alignment explanation


    Indices: 13605--13646  Score: 52
    Period size: 18  Copynumber: 2.3  Consensus size: 19

      13595 ATATATATAT

                        *      
      13605 ATATATATTTTTCTGAAAA
          1 ATATATATTTTTATGAAAA

                                
      13624 ATAT-TATTTTTAT-AAATA
          1 ATATATATTTTTATGAAA-A

                 
      13642 ATATA
          1 ATATA

      13647 AAAGTCCTCA


Statistics
Matches: 20,  Mismatches: 1, Indels: 4
        0.80            0.04        0.16

Matches are distributed among these distances:
  17    3  0.15
  18   13  0.65
  19    4  0.20

ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50


Consensus pattern (19 bp):   
ATATATATTTTTATGAAAA

Found at i:23565 original size:23 final size:23

Alignment explanation


    Indices: 23524--23567  Score: 70
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      23514 AAATAAAAGT

                         *         
      23524 ATAATATAATATATAATATTAGA
          1 ATAATATAATATAGAATATTAGA

                          *      
      23547 ATAATATAATATAGCATATTA
          1 ATAATATAATATAGAATATTA

      23568 TTATGAGTAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39


Consensus pattern (23 bp):   
ATAATATAATATAGAATATTAGA
Done.