Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008921.1 Hibiscus syriacus cultivar Beakdansim tig00112225_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: 578760
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


File 3 of 3

Found at i:565970 original size:61 final size:61

Alignment explanation


    Indices: 565838--565972  Score: 148
    Period size: 61  Copynumber: 2.2  Consensus size: 61

     565828 CGCTATGTAA

                        *   *        *                 * *          **   
     565838 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
          1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCAATT

                 *             *            *                              
     565899 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAATT
          1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT--CAATT

                         
     565962 -T-GCGTTGCGAT
          1 ATCGCGTTGCGAT

     565973 TTACTTATTC


Statistics
Matches: 61,  Mismatches: 11, Indels: 4
        0.80            0.14        0.05

Matches are distributed among these distances:
  61   57  0.93
  62    1  0.02
  63    3  0.05

ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33


Consensus pattern (61 bp):   
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCAATT

Found at i:566062 original size:21 final size:21

Alignment explanation


    Indices: 566022--566062  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

     566012 ATTGTATACC

                        **       
     566022 ATCGCAACGCGATTTCCAACT
          1 ATCGCAACGCGAAATCCAACT

                           *    
     566043 ATCGCAACGCGAAATGCAAC
          1 ATCGCAACGCGAAATCCAAC

     566063 GCGAATTTGC


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17


Consensus pattern (21 bp):   
ATCGCAACGCGAAATCCAACT

Found at i:572431 original size:9 final size:9

Alignment explanation


    Indices: 572409--572442  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

     572399 TAATTAATCG

                     
     572409 AAAT-TATT
          1 AAATATATT

                     
     572417 AAATATATT
          1 AAATATATT

             *       
     572426 ATATATATT
          1 AAATATATT

                    
     572435 AAATATAT
          1 AAATATAT

     572443 ATTTTTTGTA


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
   8    4  0.17
   9   19  0.83

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (9 bp):   
AAATATATT

Found at i:578265 original size:20 final size:22

Alignment explanation


    Indices: 578236--578275  Score: 57
    Period size: 20  Copynumber: 1.9  Consensus size: 22

     578226 AGTTTATTAT

                                  
     578236 TTAATATTTT-TT-TATTTTAA
          1 TTAATATTTTATTATATTTTAA

                 *              
     578256 TTAATTTTTTATTATATTTT
          1 TTAATATTTTATTATATTTT

     578276 GAGAGTCATG


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    9  0.53
  21    2  0.12
  22    6  0.35

ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72


Consensus pattern (22 bp):   
TTAATATTTTATTATATTTTAA

Done.