Markers + reference

Melanosciadium

3 species · Apiaceae · Apiales

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Species 3
Genome length 164–165 kb
Candidate markers 294
Primer pairs 90

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 294 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 196 0.0306 1.00 62.7 yes View details
rpoC1 LSC 2820 0.0032 1.00 50.6 yes View details
ycf3 LSC 1999 0.0033 1.00 46.3 yes View details
trnL-UAA-trnF-GAA LSC 369 0.0092 0.98 61.5 yes View details
psbE-petL LSC 1005 0.0080 1.00 66.6 yes View details
petB IRb 1403 0.0062 1.00 49.5 yes View details
ycf1 IRb 1965 0.0037 1.00 52.9 no View details
ndhF SSC 2229 0.0045 1.00 52.1 yes View details
ndhF-rpl32 SSC 1024 0.0104 1.00 52.2 yes View details
ycf1 SSC 5448 0.0059 1.00 42.2 yes View details
petB IRa 489 0.0000 1.00 31.7 no View details
petB-trnH-GUG LSC 1742 0.1987 0.89 84.5 no View details
trnC-GCA-petN LSC 693 0.0077 1.00 65.1 yes View details
trnS-GCU-trnG-UCC LSC 561 0.0071 1.00 63.3 yes View details
petA-psbJ LSC 938 0.0057 0.99 62.9 yes View details
petN-psbM LSC 1148 0.0047 0.99 62.3 yes View details
rpl20-rps12 LSC 780 0.0034 1.00 61.2 yes View details
ycf3-trnS-GGA LSC 819 0.0033 1.00 61.1 yes View details
atpF-atpH LSC 299 0.0090 0.99 61.0 yes View details
rbcL-accD LSC 639 0.0077 0.95 61.0 yes View details
trnT-UGU-trnL-UAA LSC 792 0.0034 1.00 60.9 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 90 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 CCTCTAGACCTAGCTGCTGT 263–267 1.000 81.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 313–317 1.000 81.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 327–331 1.000 80.9
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 326–330 1.000 80.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 328–332 1.000 80.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GGGGGTTACTCGAACGAATC 648–661 1.000 80.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGGGGTTACTCGAACGAATC 697–710 1.000 79.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TAAGGGGGTTACTCGAACGA 651–664 1.000 79.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TAAGGGGGTTACTCGAACGA 700–713 1.000 78.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGGGGGTTACTCGAACGAAT 649–662 1.000 77.4
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG GCCTGGTTGTAGCATTAGCA 407–415 1.000 79.4
atpF-atpH_p2 atpF-atpH CCAGTGGCCTAAAGAAACGA GCCTGGTTGTAGCATTAGCA 380–388 1.000 79.1
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 409–417 1.000 78.0
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TGAGGCGGAGGGAAAAATAC 478–486 1.000 77.7
atpF-atpH_p5 atpF-atpH CCAGTGGCCTAAAGAAACGA TGAGGCGGAGGGAAAAATAC 451–459 1.000 77.4
rpoC1_p1 rpoC1 CCGTCCTAGTTGAATCGGAG TTGCTCGTTCGAGAACTACG 2987–2989 1.000 76.2
rpoC1_p2 rpoC1 CCGTCCTAGTTGAATCGGAG ACGATCTTTGGCTCTGGAAC 2970–2972 1.000 75.7
rpoC1_p3 rpoC1 CCGTCCTAGTTGAATCGGAG TTCGATTGCTCGTTCGAGAA 2992–2994 1.000 73.8
rpoC1_p4 rpoC1 CCGTCCTAGTTGAATCGGAG TTTCGATTGCTCGTTCGAGA 2993–2995 1.000 73.8
rpoC1_p5 rpoC1 CCGTCCTAGTTGAATCGGAG CGATTGCTCGTTCGAGAACT 2990–2992 1.000 73.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 740–758 1.000 79.9
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 801–819 1.000 78.2
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 758–776 1.000 77.7
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 819–837 1.000 76.0
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 739–757 1.000 74.0
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATCC 1316–1322 1.000 78.9
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATCC 1255–1261 1.000 77.4
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT GCTACTGCACTGTTCATCCT 1315–1321 1.000 76.6
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT GCTACTGCACTGTTCATCCT 1254–1260 1.000 75.0
petN-psbM_p5 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATCC 1317–1323 1.000 73.0

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
Melanosciadium angelicifolium NC_063839.1 163802 View on NCBI ↗
Melanosciadium jinzhaiensis ON117808.1 164544 View on NCBI ↗
Melanosciadium tsinlingensis NC_057140.1 163618 View on NCBI ↗