Markers + reference

Dracula

3 species · Orchidaceae · Asparagales

Back to catalogue

Species 3
Genome length 157–158 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 505 0.0053 1.00 48.1 yes View details
atpB-rbcL LSC 1071 0.0299 1.00 65.3 yes View details
accD-psaI LSC 864 0.0054 1.00 49.7 yes View details
rps11 LSC 417 0.0000 1.00 25.5 yes View details
rps19 IRb 279 0.0024 1.00 41.5 yes View details
ycf1 IRb 1035 0.0000 1.00 32.0 no View details
ndhF SSC 2253 0.0009 1.00 45.2 yes View details
ccsA SSC 987 0.0007 1.00 46.7 yes View details
ndhE SSC 306 0.0000 1.00 29.3 yes View details
ndhA SSC 2187 0.0009 1.00 39.5 yes View details
ycf1 SSC 5439 0.0006 1.00 40.4 yes View details
rps19 IRa 279 0.0024 1.00 41.5 no View details
trnH-GUG-rpl2 IRb 43 0.0155 1.00 49.9 yes View details
rpl2-trnH-GUG IRa 43 0.0155 1.00 49.9 yes View details
rpl16 LSC 1656 0.0004 1.00 48.7 yes View details
cemA LSC 690 0.0019 1.00 47.5 yes View details
ndhC-trnV-UAC LSC 772 0.0017 1.00 47.4 yes View details
clpP1-psbB LSC 761 0.0009 1.00 47.4 yes View details
trnS-GCU-trnG-UCC LSC 995 0.0013 1.00 47.1 yes View details
psbE-petL LSC 1170 0.0011 1.00 47.1 yes View details
rps4 LSC 606 0.0011 1.00 47.0 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbK-psbI_p1 psbK-psbI CTTTGTTTGGCAAGCTGCTT ACGCCCCGGATCATTAGATA 627–629 1.000 79.8
psbK-psbI_p2 psbK-psbI CTTTGTTTGGCAAGCTGCTT TACGCCCCGGATCATTAGAT 628–630 1.000 79.8
psbK-psbI_p3 psbK-psbI AATCGTAGACGTTATGCCGG ACGCCCCGGATCATTAGATA 675–677 1.000 79.1
psbK-psbI_p4 psbK-psbI AATCGTAGACGTTATGCCGG TACGCCCCGGATCATTAGAT 676–678 1.000 79.1
psbK-psbI_p5 psbK-psbI CGTTATGCCGGTTATCCCTT ACGCCCCGGATCATTAGATA 666–668 1.000 78.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 1064 1.000 51.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1063 1.000 51.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 1067 1.000 50.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 1066 1.000 50.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 1065 1.000 50.8
rps4_p1 rps4 AATGAGATAGGGCACGAGGT TGAGTTTTGCTTTGCTGATTCT 784 1.000 55.1
rps4_p2 rps4 TGAGATAGGGCACGAGGTAC TGAGTTTTGCTTTGCTGATTCT 782 1.000 54.2
rps4_p3 rps4 GAATGAGATAGGGCACGAGG TGAGTTTTGCTTTGCTGATTCT 785 1.000 53.1
rps4_p4 rps4 AATGAGATAGGGCACGAGGT AGTGAATCAAAAAGGAGCCT 723 1.000 53.1
rps4_p5 rps4 AATGAGATAGGGCACGAGGT TGAAAGTGAATCAAAAAGGAGCC 727 1.000 52.9
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TCTGGACCTTCCCTAATCGG AGAAGGTCTACGGTTCGAGT 921 1.000 76.9
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TCTGGACCTTCCCTAATCGG AGCCCAATGCAACAAAATGC 1003 1.000 74.7
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TCTGGACCTTCCCTAATCGG GAAGGTCTACGGTTCGAGTC 920 1.000 74.2
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TCTGGACCTTCCCTAATCGG GTTCGAGTCCGTATAGCCCT 909 1.000 73.0
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TCTGGACCTTCCCTAATCGG GAAAGAGCCCAATGCAACAA 1008 1.000 71.9
trnV-UAC_p1 trnV-UAC CATCGGGTCCATTGGAATGA TGTGGGATTCTGGGATAACCT 812 1.000 68.3
trnV-UAC_p2 trnV-UAC CATCGGGTCCATTGGAATGA TGTGGGATTCTGGGATAACC 812 1.000 66.1
trnV-UAC_p3 trnV-UAC CCATCGGGTCCATTGGAATG TGTGGGATTCTGGGATAACCT 813 1.000 65.6
trnV-UAC_p4 trnV-UAC TCCATCGGGTCCATTGGAAT TGTGGGATTCTGGGATAACCT 814 1.000 64.8
trnV-UAC_p5 trnV-UAC CATCGGGTCCATTGGAATGA GTGGGATTCTGGGATAACCT 811 1.000 63.6
atpB-rbcL_p1 atpB-rbcL ATCTTGCCCGGTGGAAAAAT ACCAGCTTTAAATCCAACGC 1238 1.000 74.5
atpB-rbcL_p2 atpB-rbcL ATCTTGCCCGGTGGAAAAAT AGCTTTAAATCCAACGCTTGC 1235 1.000 74.2
atpB-rbcL_p3 atpB-rbcL ATCTTGCCCGGTGGAAAAAT GCTTTAAATCCAACGCTTGCT 1234 1.000 74.2
atpB-rbcL_p4 atpB-rbcL TGGGCCAATAATTTGAGCGA ACCAGCTTTAAATCCAACGC 1206 1.000 74.0
atpB-rbcL_p5 atpB-rbcL TGGGCCAATAATTTGAGCGA GCTTTAAATCCAACGCTTGCT 1202 1.000 73.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Dracula astuta NC_086627.1 157516 View on NCBI ↗
Dracula erythrochaete NC_085157.1 157517 View on NCBI ↗
Dracula mendozae NC_085156.1 157484 View on NCBI ↗