Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01003544.1 Hibiscus syriacus cultivar Beakdansim tig00007475_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: 48270
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:4205 original size:31 final size:29

Alignment explanation


    Indices: 4139--4224  Score: 88
    Period size: 30  Copynumber: 2.9  Consensus size: 29

       4129 TTGAAAGAAC

                       *    *             
       4139 AATTAT-TAATCTATTCATTTATATTTTAT
          1 AATTATATAATATATTGA-TTATATTTTAT

                          *               
       4168 AATTATATAAGTATGTTGATTATATTTT-T
          1 AATTATATAA-TATATTGATTATATTTTAT

                                         
       4197 AATTTTATATAATATATTGATTA-ATTTT
          1 AA--TTATATAATATATTGATTATATTTT

       4225 GTTCGTCATT


Statistics
Matches: 49,  Mismatches: 4, Indels: 8
        0.80            0.07        0.13

Matches are distributed among these distances:
  29   14  0.29
  30   22  0.45
  31   13  0.27

ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57


Consensus pattern (29 bp):   
AATTATATAATATATTGATTATATTTTAT

Found at i:15655 original size:89 final size:89

Alignment explanation


    Indices: 15515--15678  Score: 265
    Period size: 89  Copynumber: 1.8  Consensus size: 89

      15505 GACTGCATAA

                                   *                 *                      *
      15515 GCATTCATAGAATGCTCTATACTTATGTTATCATGTTTGACGTCTGCCATGAAATTTATATCAAT
          1 GCATTCATAGAATGCTCTATACTGATGTTATCATGTTTGACATCTGCCATGAAATTTATATCAAG

                                    
      15580 ATGTCATTAATATTAGGAAGGACT
         66 ATGTCATTAATATTAGGAAGGACT

                                            *       *     *                  
      15604 GCATTCATAGAATGCTCTATACTGATGTTATCTTGTTTGATATCTGTCATGAAATTTATATCAAG
          1 GCATTCATAGAATGCTCTATACTGATGTTATCATGTTTGACATCTGCCATGAAATTTATATCAAG

                 *    
      15669 ATGTCTTTAA
         66 ATGTCATTAA

      15679 ATCTTGAAAG


Statistics
Matches: 68,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  89   68  1.00

ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40


Consensus pattern (89 bp):   
GCATTCATAGAATGCTCTATACTGATGTTATCATGTTTGACATCTGCCATGAAATTTATATCAAG
ATGTCATTAATATTAGGAAGGACT

Found at i:31191 original size:46 final size:46

Alignment explanation


    Indices: 31140--31413  Score: 539
    Period size: 46  Copynumber: 6.0  Consensus size: 46

      31130 TTAAGTAACG

                                                          
      31140 TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCTTT
          1 TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCTTT

                                                          
      31186 TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCTTT
          1 TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCTTT

                                                          
      31232 TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCTTT
          1 TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCTTT

                                  *                       
      31278 TTAATTATTAATAGGGTAACTTGCATGTTTGATAATCAAGCTCTTT
          1 TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCTTT

                                                          
      31324 TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCTTT
          1 TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCTTT

                                                        
      31370 TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCT
          1 TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCT

      31414 GTTTGATTTT


Statistics
Matches: 226,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  46  226  1.00

ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43


Consensus pattern (46 bp):   
TTAATTATTAATAGGGTAACTTACATGTTTGATAATCAAGCTCTTT

Found at i:36851 original size:15 final size:16

Alignment explanation


    Indices: 36815--36853  Score: 62
    Period size: 16  Copynumber: 2.5  Consensus size: 16

      36805 AGAGCCTCTG

                            
      36815 AATCATTCAGCATTTA
          1 AATCATTCAGCATTTA

                       *    
      36831 AATCATTCAGCGTTT-
          1 AATCATTCAGCATTTA

                    
      36846 AATCATTC
          1 AATCATTC

      36854 TGAAGTAAAC


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15    8  0.36
  16   14  0.64

ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38


Consensus pattern (16 bp):   
AATCATTCAGCATTTA
Done.