Markers + reference

Paraphlomis

31 species · Lamiaceae · Lamiales

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Species 31
Genome length 152–152 kb
Candidate markers 271
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1059 0.0011 1.00 29.2 yes View details
trnS-GCU-trnG-UCC LSC 692 0.0075 1.00 55.2 yes View details
trnT-GGU-psbD LSC 1249 0.0035 1.00 50.6 yes View details
rbcL LSC 1455 0.0048 1.00 53.7 yes View details
petA-psbJ LSC 1044 0.0088 1.00 63.5 yes View details
ndhF SSC 2223 0.0032 1.00 40.1 yes View details
ndhF-rpl32 SSC 504 0.0090 1.00 62.9 yes View details
rpl32-trnL-UAG SSC 723 0.0077 1.00 51.7 yes View details
ccsA SSC 972 0.0046 1.00 36.3 yes View details
psaC-ndhE SSC 262 0.0074 1.00 43.0 yes View details
ycf1 SSC 5553 0.0041 1.00 55.7 yes View details
trnH-GUG-psbA LSC 233 0.0271 0.99 67.8 yes View details
psbE-petL LSC 928 0.0038 1.00 61.4 yes View details
trnC-GCA-petN LSC 831 0.0039 1.00 60.6 yes View details
ndhE-ndhG SSC 218 0.0084 1.00 58.3 yes View details
ccsA-ndhD SSC 183 0.0147 0.99 57.9 yes View details
trnK-UUU-rps16 LSC 927 0.0036 1.00 57.4 yes View details
ndhC-trnV-UAC LSC 965 0.0052 1.00 57.2 yes View details
matK LSC 1536 0.0039 1.00 56.2 yes View details
ycf3 LSC 1958 0.0026 1.00 55.9 yes View details
atpF LSC 1222 0.0038 1.00 54.5 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 105 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 CAACCGTGCTAACCTTGGTA 349–359 1.000 85.8
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATCAACCGTGCTAACCTTGG 351–361 1.000 85.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 362–372 1.000 85.5
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 363–373 1.000 85.4
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CAACCGTGCTAACCTTGGTA 364–374 1.000 85.4
psbA_p1 psbA GATCCACTTGGCTACATCCG GAAAGCCGTGTGCAATGAAA 1665–1678 1.000 80.3
psbA_p2 psbA CAATCCACTGCCTTGATCCA GAAAGCCGTGTGCAATGAAA 1679–1692 1.000 80.2
psbA_p3 psbA AATCCACTGCCTTGATCCAC GAAAGCCGTGTGCAATGAAA 1678–1691 1.000 80.2
psbA_p4 psbA ACAATCCACTGCCTTGATCC GAAAGCCGTGTGCAATGAAA 1680–1693 1.000 80.2
psbA_p5 psbA GATCCACTTGGCTACATCCG CTAGTTCCGGGTTCGAATCC 1571–1584 1.000 79.7
matK_p1 matK GGATCTTTTTATCTCTCGATCCA AGTTTATCTGTCCCCGAGGT 1709–1717 1.000 42.5
matK_p2 matK TGGATCTTTTTATCTCTCGATCC AGTTTATCTGTCCCCGAGGT 1710–1718 1.000 42.5
matK_p3 matK TTGGATCTTTTTATCTCTCGATCC AGTTTATCTGTCCCCGAGGT 1711–1719 1.000 42.5
matK_p4 matK ACATCAACATTTCAGAATAGTGGA AGTTTATCTGTCCCCGAGGT 1743–1751 1.000 42.4
matK_p5 matK ACATTTCAGAATAGTGGAAATCCA AGTTTATCTGTCCCCGAGGT 1737–1745 1.000 42.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGAACTTCCGCCTAATCAA 979–997 1.000 71.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTTCCGCCTAATCAA 978–996 1.000 71.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGGAACTTCCGCCTAATCAA 988–1006 1.000 70.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTTCCGCCTAATCAAA 978–996 1.000 69.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AGGAACTTCCGCCTAATCAA 993–1011 0.968 68.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 683–771 1.000 59.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 682–770 1.000 59.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 686–774 1.000 58.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 685–773 1.000 58.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 684–772 1.000 58.1
atpF_p1 atpF ATTTCGTCGGCTTGAATGGT AAGAGGGGCAAAGTGATAGA 1393–1405 0.968 62.9
atpF_p2 atpF ATTTCGTCGGCTTGAATGGT AGAGGGGCAAAGTGATAGAA 1392–1404 0.968 62.9
atpF_p3 atpF GTCGGCTTGAATGGTTACCA AAGAGGGGCAAAGTGATAGA 1388–1400 0.968 62.9
atpF_p4 atpF GTCGGCTTGAATGGTTACCA AGAGGGGCAAAGTGATAGAA 1387–1399 0.968 62.9
atpF_p5 atpF TCGTCGGCTTGAATGGTTAC AGAGGGGCAAAGTGATAGAA 1389–1401 0.968 62.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (31)

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

Species Accession Length (bp) Link
Paraphlomis albida var. albida OR565920.1 152224 View on NCBI ↗
Paraphlomis albida var. brevidens OR565938.1 152206 View on NCBI ↗
Paraphlomis albiflora OR565954.1 152003 View on NCBI ↗
Paraphlomis albiflora var. biflora OR565950.1 152028 View on NCBI ↗
Paraphlomis albotomentosa OR565962.1 152206 View on NCBI ↗
Paraphlomis coronata OR565914.1 152201 View on NCBI ↗
Paraphlomis foliata NC_085509.1 152210 View on NCBI ↗
Paraphlomis foliata subsp. montigena OR565931.1 152219 View on NCBI ↗
Paraphlomis formosana OR565953.1 152198 View on NCBI ↗
Paraphlomis gracilis OR565927.1 152215 View on NCBI ↗
Paraphlomis gracilis var. lutienensis OR565930.1 152234 View on NCBI ↗
Paraphlomis hirsutissima OR565958.1 152222 View on NCBI ↗
Paraphlomis hispida NC_085510.1 152210 View on NCBI ↗
Paraphlomis intermedia OR565934.1 152128 View on NCBI ↗
Paraphlomis javanica NC_085355.1 152227 View on NCBI ↗
Paraphlomis javanica var. pteropoda OR565943.1 152203 View on NCBI ↗
Paraphlomis jinggangshanensis OR565956.1 152194 View on NCBI ↗
Paraphlomis kuankuoshuiensis OR565939.1 152141 View on NCBI ↗
Paraphlomis kwangtungensis OR565963.1 152066 View on NCBI ↗
Paraphlomis lanceolata OR565928.1 152162 View on NCBI ↗
Paraphlomis lancidentata OR565933.1 152199 View on NCBI ↗
Paraphlomis longicalyx OR565925.1 152156 View on NCBI ↗
Paraphlomis membranacea OR565959.1 152253 View on NCBI ↗
Paraphlomis nana OR565913.1 151991 View on NCBI ↗
Paraphlomis patentisetulosa OR565932.1 152204 View on NCBI ↗
Paraphlomis paucisetosa OR565915.1 152210 View on NCBI ↗
Paraphlomis reflexa OR565916.1 152127 View on NCBI ↗
Paraphlomis seticalyx OR565940.1 152208 View on NCBI ↗
Paraphlomis setulosa OR565960.1 152254 View on NCBI ↗
Paraphlomis strictiflora OR565937.1 152248 View on NCBI ↗
Paraphlomis yingdeensis OR565948.1 152183 View on NCBI ↗