Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001281.1 Hibiscus syriacus cultivar Beakdansim tig00002515_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: 106746
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


File 2 of 2

Found at i:92442 original size:42 final size:41

Alignment explanation


    Indices: 92377--92483  Score: 133
    Period size: 42  Copynumber: 2.6  Consensus size: 41

      92367 TAGGAATGTA

                 *       *            *          *   
      92377 ACCCTACGGAGATGGCATATGAACTGGTGAGCTGGGCGTAT
          1 ACCCTGCGGAGATAGCATATGAACTGATGAGCTGGGCATAT

                                          * *         
      92418 ATCCCTGCGGAGATAGCATATGAACTGATGGGTTGGGCATAT
          1 A-CCCTGCGGAGATAGCATATGAACTGATGAGCTGGGCATAT

                               *    
      92460 ACCCTTGCGGAGATAGCATCTGAA
          1 ACCC-TGCGGAGATAGCATATGAA

      92484 ATTGTGGGCT


Statistics
Matches: 57,  Mismatches: 7, Indels: 3
        0.85            0.10        0.04

Matches are distributed among these distances:
  41    4  0.07
  42   53  0.93

ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23


Consensus pattern (41 bp):   
ACCCTGCGGAGATAGCATATGAACTGATGAGCTGGGCATAT

Found at i:92505 original size:42 final size:42

Alignment explanation


    Indices: 92383--92505  Score: 124
    Period size: 42  Copynumber: 2.9  Consensus size: 42

      92373 TGTAACCCTA

                   *            *  *      **           
      92383 CGGAGATGGCATATGAACTGGTGAGCTGGGCGTATATCCC-TG
          1 CGGAGATAGCATATGAACTGATGGGCTGGGAATATA-CCCTTG

                                     *    *           
      92425 CGGAGATAGCATATGAACTGATGGGTTGGGCATATACCCTTG
          1 CGGAGATAGCATATGAACTGATGGGCTGGGAATATACCCTTG

                        *     *               *     
      92467 CGGAGATAGCATCTGAAATTG-TGGGCTGGGAATGTACCC
          1 CGGAGATAGCATATG-AACTGATGGGCTGGGAATATACCC

      92506 CTGTGGCCTC


Statistics
Matches: 69,  Mismatches: 10, Indels: 4
        0.83            0.12        0.05

Matches are distributed among these distances:
  41    3  0.04
  42   62  0.90
  43    4  0.06

ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24


Consensus pattern (42 bp):   
CGGAGATAGCATATGAACTGATGGGCTGGGAATATACCCTTG

Found at i:93081 original size:17 final size:17

Alignment explanation


    Indices: 93059--93094  Score: 56
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      93049 AAACTGAAAC

                              
      93059 ATAAATAT-ATAATTCTA
          1 ATAAATATAAT-ATTCTA

                             
      93076 ATAAATATAATATTCTA
          1 ATAAATATAATATTCTA

              
      93093 AT
          1 AT

      93095 TGTATCAAGC


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

Matches are distributed among these distances:
  17   16  0.89
  18    2  0.11

ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42


Consensus pattern (17 bp):   
ATAAATATAATATTCTA

Found at i:94215 original size:4 final size:4

Alignment explanation


    Indices: 94208--94232  Score: 50
    Period size: 4  Copynumber: 6.2  Consensus size: 4

      94198 ATAATTAGCA

                                           
      94208 TAAT TAAT TAAT TAAT TAAT TAAT T
          1 TAAT TAAT TAAT TAAT TAAT TAAT T

      94233 TAAATAAATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   21  1.00

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


Consensus pattern (4 bp):   
TAAT

Found at i:102551 original size:19 final size:19

Alignment explanation


    Indices: 102513--102552  Score: 55
    Period size: 19  Copynumber: 2.1  Consensus size: 19

     102503 CGAATAAATT

                           *   
     102513 AATCGAATATATAATTTTA
          1 AATCGAATATATAATCTTA

                                
     102532 AATCGAATATA-ATATCTTA
          1 AATCGAATATATA-ATCTTA

              
     102551 AA
          1 AA

     102553 ATTCAATAGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  18    1  0.05
  19   18  0.95

ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38


Consensus pattern (19 bp):   
AATCGAATATATAATCTTA

Done.