Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01003163.1 Hibiscus syriacus cultivar Beakdansim tig00006657_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: 157297
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


File 2 of 2

Found at i:147503 original size:34 final size:34

Alignment explanation


    Indices: 147429--147503  Score: 80
    Period size: 34  Copynumber: 2.2  Consensus size: 34

     147419 TAATACATAT

                  *         *    *     *      
     147429 AATAAACATAAATTTATAAATTTAAATTATATAA
          1 AATAAAAATAAATTTAAAAATATAAATAATATAA

            **                                 
     147463 TCTAAAAATAAATTTTAAAAATATAAA-AATATAA
          1 AATAAAAATAAA-TTTAAAAATATAAATAATATAA

                   
     147497 AATAAAA
          1 AATAAAA

     147504 TTATAAAATT


Statistics
Matches: 32,  Mismatches: 8, Indels: 2
        0.76            0.19        0.05

Matches are distributed among these distances:
  34   20  0.62
  35   12  0.38

ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33


Consensus pattern (34 bp):   
AATAAAAATAAATTTAAAAATATAAATAATATAA

Found at i:147552 original size:20 final size:21

Alignment explanation


    Indices: 147517--147559  Score: 70
    Period size: 20  Copynumber: 2.0  Consensus size: 21

     147507 TAAAATTACA

                                  
     147517 ATTAAAATCAAAATAATTTAAG
          1 ATTAAAAT-AAAATAATTTAAG

                                 
     147539 ATTAAAAT-AAATAATTTAAG
          1 ATTAAAATAAAATAATTTAAG

             
     147559 A
          1 A

     147560 AATAATTTAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  20   13  0.62
  22    8  0.38

ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33


Consensus pattern (21 bp):   
ATTAAAATAAAATAATTTAAG

Found at i:148435 original size:13 final size:13

Alignment explanation


    Indices: 148419--148463  Score: 56
    Period size: 13  Copynumber: 3.5  Consensus size: 13

     148409 TTAAAAATAA

                         
     148419 AAAAATATAAAAT
          1 AAAAATATAAAAT

                         
     148432 AAAAATATAAAAT
          1 AAAAATATAAAAT

            * *          
     148445 TACAAT-TAAAAT
          1 AAAAATATAAAAT

            *      
     148457 CAAAATA
          1 AAAAATA

     148464 ATTAAGATTA


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  12   10  0.37
  13   17  0.63

ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24


Consensus pattern (13 bp):   
AAAAATATAAAAT

Found at i:148467 original size:21 final size:19

Alignment explanation


    Indices: 148449--148490  Score: 57
    Period size: 19  Copynumber: 2.1  Consensus size: 19

     148439 TAAAATTACA

                                 
     148449 ATTAAAATCAAAATAATTAAG
          1 ATTAAAAT--AAATAATTAAG

                                
     148470 ATTAAAATAAATAATTGAAG
          1 ATTAAAATAAATAATT-AAG

             
     148490 A
          1 A

     148491 AATAATTTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  19    8  0.40
  20    4  0.20
  21    8  0.40

ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29


Consensus pattern (19 bp):   
ATTAAAATAAATAATTAAG

Found at i:149397 original size:13 final size:13

Alignment explanation


    Indices: 149381--149410  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

     149371 AGAGTGGAGA

                         
     149381 ATGAGAAAAATCC
          1 ATGAGAAAAATCC

                         
     149394 ATGAGAAAAATCC
          1 ATGAGAAAAATCC

                
     149407 ATGA
          1 ATGA

     149411 ACCCCTCCTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.53, C:0.13, G:0.17, T:0.17


Consensus pattern (13 bp):   
ATGAGAAAAATCC

Done.