Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008464.1 Hibiscus syriacus cultivar Beakdansim tig00111277_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: 593006
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 4 of 4

Found at i:574428 original size:31 final size:31

Alignment explanation


    Indices: 574385--574478  Score: 154
    Period size: 31  Copynumber: 3.0  Consensus size: 31

     574375 AGGGTCGAGG

                                           
     574385 GTTTACCTATGTTCTTCGGGACATATGGACT
          1 GTTTACCTATGTTCTTCGGGACATATGGACT

                *                          
     574416 GTTTGCCTATGTTCTTCGGGACATATGGACT
          1 GTTTACCTATGTTCTTCGGGACATATGGACT

                     *                      
     574447 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
          1 GTTTACCTATGTTCTTCGGGA-CATATGGACT

             
     574478 G
          1 G

     574479 ATCCTTTAGG


Statistics
Matches: 59,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  31   58  0.98
  32    1  0.02

ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38


Consensus pattern (31 bp):   
GTTTACCTATGTTCTTCGGGACATATGGACT

Found at i:575386 original size:37 final size:37

Alignment explanation


    Indices: 575317--575394  Score: 93
    Period size: 37  Copynumber: 2.1  Consensus size: 37

     575307 ACCATAGAAT

                     *              * **         
     575317 AGAAGCCCAGAATCCCTACATCATGTTGAAACTCTAA
          1 AGAAGCCCACAATCCCTACATCATATCAAAACTCTAA

                   *       *                 *   
     575354 AGAAGCCTACAATCCTTACATCATATCAAAACTTTAA
          1 AGAAGCCCACAATCCCTACATCATATCAAAACTCTAA

                
     575391 AGAA
          1 AGAA

     575395 ACCATAGAAG


Statistics
Matches: 34,  Mismatches: 7, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  37   34  1.00

ACGTcount: A:0.42, C:0.24, G:0.10, T:0.23


Consensus pattern (37 bp):   
AGAAGCCCACAATCCCTACATCATATCAAAACTCTAA

Found at i:577429 original size:33 final size:36

Alignment explanation


    Indices: 577340--577409  Score: 117
    Period size: 36  Copynumber: 2.0  Consensus size: 36

     577330 AACATCTACC

                              *                 
     577340 AAAC-TTTACCAAACTTTAAAAAACATTTTTCAAAG
          1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG

                                                
     577375 AAACATTTACCAAACTTTGAAAAACA-TTTTCAAAG
          1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG

     577410 TTGATTGCCA


Statistics
Matches: 33,  Mismatches: 1, Indels: 2
        0.92            0.03        0.06

Matches are distributed among these distances:
  35   13  0.39
  36   20  0.61

ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30


Consensus pattern (36 bp):   
AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG

Found at i:579568 original size:19 final size:20

Alignment explanation


    Indices: 579531--579568  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

     579521 TTTTTTTATA

                       *        
     579531 TGGGGGAATCGGTTCCCCCC
          1 TGGGGGAATCGATTCCCCCC

                  *           
     579551 TGGGGGTATCGATTCCCC
          1 TGGGGGAATCGATTCCCC

     579569 TCTAGCATTC


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24


Consensus pattern (20 bp):   
TGGGGGAATCGATTCCCCCC

Found at i:585713 original size:23 final size:23

Alignment explanation


    Indices: 585687--585731  Score: 63
    Period size: 23  Copynumber: 2.0  Consensus size: 23

     585677 CACCACAGCT

                *                  
     585687 CGTATAAATGCACCGAAGTGCCG
          1 CGTAGAAATGCACCGAAGTGCCG

                   *       *      
     585710 CGTAGAATTGCACCGTAGTGCC
          1 CGTAGAAATGCACCGAAGTGCC

     585732 ATATAATAAT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20


Consensus pattern (23 bp):   
CGTAGAAATGCACCGAAGTGCCG

Found at i:586389 original size:19 final size:20

Alignment explanation


    Indices: 586352--586389  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

     586342 TTTTTTTATA

                       *        
     586352 TGGGGGAATCGGTTCCCCCC
          1 TGGGGGAATCGATTCCCCCC

                  *           
     586372 TGGGGGTATCGATTCCCC
          1 TGGGGGAATCGATTCCCC

     586390 TCTAGCATTC


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24


Consensus pattern (20 bp):   
TGGGGGAATCGATTCCCCCC

Found at i:592944 original size:16 final size:17

Alignment explanation


    Indices: 592916--592951  Score: 65
    Period size: 16  Copynumber: 2.2  Consensus size: 17

     592906 TTGTATCGCG

                             
     592916 ACAAAATTTTACTATTC
          1 ACAAAATTTTACTATTC

                             
     592933 ACAAAA-TTTACTATTC
          1 ACAAAATTTTACTATTC

               
     592949 ACA
          1 ACA

     592952 TGAATAGTAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  16   13  0.68
  17    6  0.32

ACGTcount: A:0.44, C:0.19, G:0.00, T:0.36


Consensus pattern (17 bp):   
ACAAAATTTTACTATTC

Done.