Markers + reference

Philodendron

2 species · Araceae · Alismatales

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Species 2
Genome length 168–169 kb
Candidate markers 264
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5673 0.4123 0.79 73.1 yes View details
ndhH SSC 1182 0.4919 0.79 79.1 yes View details
ndhA SSC 2192 0.4719 0.90 80.8 yes View details
ndhI SSC 543 0.4885 0.88 80.4 yes View details
ndhD SSC 1503 0.4798 0.74 77.7 yes View details
rpl32-ndhF SSC 1278 0.4585 0.92 82.8 yes View details
ndhF SSC 2229 0.4597 0.84 78.9 yes View details
psbC-trnS-UGA LSC 123 0.0984 0.99 88.0 yes View details
petD-rpoA LSC 191 0.0802 0.98 82.9 yes View details
ndhE-psaC SSC 619 0.4368 0.92 82.9 yes View details
rpl22-rps19 LSC 98 0.1327 1.00 82.1 yes View details
ndhI-ndhG SSC 904 0.4231 0.87 81.6 yes View details
rrn4.5-rrn5 SSC 224 0.0491 1.00 80.7 yes View details
rrn5-rrn4.5 SSC 224 0.0491 1.00 80.7 yes View details
ccsA SSC 972 0.4434 0.84 80.4 yes View details
ndhF-trnN SSC 2286 0.2633 0.89 80.4 yes View details
trnH-GUG-psbA LSC 714 0.0691 0.93 79.9 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TAGTTGACAGTCAGGGTCGT 881–930 1.000 87.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 780–829 1.000 87.1
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TAGTTGACAGTCAGGGTCGT 895–944 1.000 87.0
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TAGTTGACAGTCAGGGTCGT 894–943 1.000 86.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TAGTTGACAGTCAGGGTCGT 896–945 1.000 86.9
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGGTTCGAATCCCTCTCTCT 175–176 1.000 82.9
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 229–230 1.000 82.8
psbC-trnS-UGA_p3 psbC-trnS-UGA TTCCATGACCCCTCTTAGCT GGTTGATAGCTCCGGTCTTG 221–222 1.000 82.1
psbC-trnS-UGA_p4 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GATGGCCGAGTGGTTGATAG 240–241 1.000 82.0
psbC-trnS-UGA_p5 psbC-trnS-UGA TTGTGGGTCATTTGTGGCAT GGTTGATAGCTCCGGTCTTG 309–310 1.000 80.6
petD-rpoA_p1 petD-rpoA TTTTTGATCGGTACCGCAGT AGACATTCTACAGAAACATTTCACA 333–336 1.000 44.5
petD-rpoA_p2 petD-rpoA CGTCGTCCAGTAGCTACAAC AGACATTCTACAGAAACATTTCACA 357–360 1.000 44.2
petD-rpoA_p3 petD-rpoA TCGTCGTCCAGTAGCTACAA AGACATTCTACAGAAACATTTCACA 358–361 1.000 44.2
petD-rpoA_p4 petD-rpoA TTCGTCGTCCAGTAGCTACA AGACATTCTACAGAAACATTTCACA 359–362 1.000 44.2
petD-rpoA_p5 petD-rpoA CATTTCGTCGTCCAGTAGCT AGACATTCTACAGAAACATTTCACA 362–365 1.000 44.2
rpl22-rps19_p1 rpl22-rps19 GTACGCGGTTTACTCGAGTT GACATGCGCGAAATGACAAT 174–182 1.000 84.2
rpl22-rps19_p2 rpl22-rps19 TTCTGTACGCGGTTTACTCG GACATGCGCGAAATGACAAT 178–186 1.000 84.0
rpl22-rps19_p3 rpl22-rps19 GTACGCGGTTTACTCGAGTT GGAGAATTCGCACCTACTCG 205–213 1.000 83.5
rpl22-rps19_p4 rpl22-rps19 TTCTGTACGCGGTTTACTCG GGAGAATTCGCACCTACTCG 209–217 1.000 83.4
rpl22-rps19_p5 rpl22-rps19 GTACGCGGTTTACTCGAGTT GGGAGAATTCGCACCTACTC 206–214 1.000 82.9
rrn4.5-rrn5_p1 rrn4.5-rrn5 CAGCTGAGGCATCCTAACAG AGTATCGTCACCGCAGTAGA 341–349 1.000 81.9
rrn4.5-rrn5_p2 rrn4.5-rrn5 CAGCTGAGGCATCCTAACAG TATCGTCACCGCAGTAGAGT 339–347 1.000 81.9
rrn4.5-rrn5_p3 rrn4.5-rrn5 GCTGAGGCATCCTAACAGAC TATCGTCACCGCAGTAGAGT 337–345 1.000 81.9
rrn4.5-rrn5_p4 rrn4.5-rrn5 GTCAAGTGGAAGTGCAGTGA AGTATCGTCACCGCAGTAGA 367–375 1.000 81.7
rrn4.5-rrn5_p5 rrn4.5-rrn5 GTCAAGTGGAAGTGCAGTGA TATCGTCACCGCAGTAGAGT 365–373 1.000 81.7
ycf1_p1 ycf1 CCGAGTGGTACGAGGATTTG AATAGTCCTCGTGTCCCACA 1231 0.500 58.8
ycf1_p2 ycf1 CCGAGTGGTACGAGGATTTG ATAGTCCTCGTGTCCCACAA 1230 0.500 58.8
ycf1_p3 ycf1 GAACTCCCTTTCGGTTCTCC AATAGTCCTCGTGTCCCACA 971 0.500 58.7
ycf1_p4 ycf1 GAACTCCCTTTCGGTTCTCC ATAGTCCTCGTGTCCCACAA 970 0.500 58.7
ycf1_p5 ycf1 GGAACTCCCTTTCGGTTCTC ATAGTCCTCGTGTCCCACAA 971 0.500 58.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Philodendron hederaceum NC_064988.1 168609 View on NCBI ↗
Philodendron lanceolatum MN551187.1 167564 View on NCBI ↗