Markers + reference

Commidendrum

4 species · Asteraceae · Asterales

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Species 4
Genome length 153–153 kb
Candidate markers 262
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0006 1.00 40.4 yes View details
atpI LSC 744 0.0000 1.00 40.0 yes View details
trnR-UCU-trnG-UCC LSC 232 0.0029 1.00 36.0 yes View details
psbD LSC 1062 0.0000 1.00 25.8 yes View details
trnT-UGU-trnL-UAA LSC 655 0.0010 1.00 40.6 yes View details
psbE-petL LSC 1251 0.0009 1.00 59.6 yes View details
rps8-rpl14 LSC 190 0.0000 1.00 48.8 yes View details
rpoC2-rps2 LSC 231 0.0022 0.99 45.5 yes View details
ndhC-trnV-UAC LSC 772 0.0006 1.00 45.1 yes View details
ycf4-cemA LSC 906 0.0006 1.00 45.1 yes View details
trnL-UAG-rpl32 SSC 836 0.0006 1.00 45.1 yes View details
rps16 LSC 1148 0.0004 1.00 45.0 yes View details
ndhH SSC 1182 0.0004 1.00 45.0 yes View details
ycf3 LSC 1935 0.0003 1.00 44.0 yes View details
trnT-GGU LSC 68 0.0074 1.00 43.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA AAAAGGAGCAATAACGCCCT TATTGGTTGACACGCGCATA 1278 1.000 78.2
psbA_p2 psbA AAAAGGAGCAATAACGCCCT TGGTTGACACGCGCATATAA 1275 1.000 78.2
psbA_p3 psbA AAAAGGAGCAATAACGCCCT TTGGTTGACACGCGCATATA 1276 1.000 78.2
psbA_p4 psbA GGAGCAATAACGCCCTCTTT TGGTTGACACGCGCATATAA 1271 1.000 78.0
psbA_p5 psbA GGAGCAATAACGCCCTCTTT TTGGTTGACACGCGCATATA 1272 1.000 78.0
trnK-UUU_p1 trnK-UUU GCCGTTTGCAAAAATAAAAAGGA TCTGATTGTATCTACATACCCT 2709 1.000 40.0
trnK-UUU_p2 trnK-UUU AGCCGTTTGCAAAAATAAAAAGG TCTGATTGTATCTACATACCCT 2710 1.000 40.0
trnK-UUU_p3 trnK-UUU GCCGTTTGCAAAAATAAAAAGGA TCTGATTGTATCTACATACCCTT 2709 1.000 40.0
trnK-UUU_p4 trnK-UUU GCCGTTTGCAAAAATAAAAAGGA TTCTGATTGTATCTACATACCCT 2710 1.000 40.0
trnK-UUU_p5 trnK-UUU AGCCGTTTGCAAAAATAAAAAGG TCTGATTGTATCTACATACCCTT 2710 1.000 40.0
rps16_p1 rps16 ACGAATAGACCAAGAAAGGA TCTCTGTACCGACTGAACCA 1325 1.000 43.4
rps16_p2 rps16 ACGAATAGACCAAGAAAGGAA TCTCTGTACCGACTGAACCA 1325 1.000 42.5
rps16_p3 rps16 ACGAATAGACCAAGAAAGGAAA TCTCTGTACCGACTGAACCA 1325 1.000 40.9
rps16_p4 rps16 ACGAATAGACCAAGAAAGGA GTCTCTGTACCGACTGAACC 1326 1.000 40.5
rps16_p5 rps16 ACGAATAGACCAAGAAAGGAA GTCTCTGTACCGACTGAACC 1326 1.000 40.1
rpoC2-rps2_p1 rpoC2-rps2 TGCCTTTCAAAGAATTTCCATGA CCATGGCCAAAATGAACTCC 345–347 1.000 44.8
rpoC2-rps2_p2 rpoC2-rps2 TGCCTTTCAAAGAATTTCCATGA GGCCAAAATGAACTCCTGCT 341–343 1.000 44.3
rpoC2-rps2_p3 rpoC2-rps2 TCTTGCCTTTCAAAGAATTTCCA CCATGGCCAAAATGAACTCC 348–350 1.000 44.3
rpoC2-rps2_p4 rpoC2-rps2 TCTTGCCTTTCAAAGAATTTCCA GGCCAAAATGAACTCCTGCT 344–346 1.000 43.8
rpoC2-rps2_p5 rpoC2-rps2 TGCCTTTCAAAGAATTTCCATGA TGGCCAAAATGAACTCCTGC 342–344 1.000 42.0
atpI_p1 atpI GTCAAGTCGAGAAAGAGATGGT TTTTAGCCACGCACACATTG 871 1.000 59.2
atpI_p2 atpI GTCAAGTCGAGAAAGAGATGGT ACGCACACATTGTCTTAGGT 863 1.000 58.2
atpI_p3 atpI AGTCAAGTCGAGAAAGAGATGG TTTTAGCCACGCACACATTG 872 1.000 57.1
atpI_p4 atpI GTCAAGTCGAGAAAGAGATGGT TTTAGCCACGCACACATTGT 870 1.000 57.1
atpI_p5 atpI AGTCAAGTCGAGAAAGAGATGG ACGCACACATTGTCTTAGGT 864 1.000 56.1
trnR-UCU-trnG-UCC_p1 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 311–312 1.000 63.9
trnR-UCU-trnG-UCC_p2 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 314–315 1.000 63.6
trnR-UCU-trnG-UCC_p3 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 317–318 1.000 63.2
trnR-UCU-trnG-UCC_p4 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 320–321 1.000 63.0
trnR-UCU-trnG-UCC_p5 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 315–316 1.000 61.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Commidendrum robustum PV785969.1 152535 View on NCBI ↗
Commidendrum rotundifolium PV822555.1 152592 View on NCBI ↗
Commidendrum rugosum PV785968.1 152525 View on NCBI ↗
Commidendrum spurium PV822556.1 152608 View on NCBI ↗