Markers + reference

Nothosmyrnium

2 species · Apiaceae · Apiales

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Species 2
Genome length 141–141 kb
Candidate markers 253
Primer pairs 105

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 253 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 732 0.0169 0.97 62.0 yes View details
rps16 LSC 1091 0.0083 1.00 50.3 yes View details
atpH-atpI LSC 1149 0.0118 0.96 68.2 yes View details
petN-psbM LSC 892 0.0135 1.00 66.5 yes View details
trnE-UUC-trnT-GGU LSC 744 0.0135 0.99 67.2 yes View details
trnT-GGU-psbD LSC 1421 0.0099 1.00 64.5 yes View details
petA-psbJ LSC 642 0.0358 1.00 71.1 yes View details
petB LSC 1393 0.0057 1.00 48.1 yes View details
trnL-CAA-ndhB LSC 571 0.0160 0.99 64.1 yes View details
ycf15-trnV-GAC LSC 688 0.0160 1.00 53.4 yes View details
ndhF SSC 2247 0.0067 1.00 61.0 yes View details
rpl32-trnL-UAG SSC 939 0.0129 0.91 69.6 yes View details
atpA-atpF LSC 49 0.0408 1.00 76.0 yes View details
ndhI-ndhA SSC 93 0.0323 1.00 71.0 yes View details
rps11-rpl36 LSC 113 0.0270 0.98 66.9 yes View details
trnG-GCC-trnR-UCU LSC 139 0.0153 0.94 65.8 yes View details
ndhH-rps15 SSC 91 0.0220 1.00 65.1 yes View details
accD-psaI LSC 448 0.0092 0.98 63.2 yes View details
trnT-UGU-trnL-UAA LSC 823 0.0074 0.99 62.9 yes View details
rps12-ycf15 LSC 968 0.0111 0.75 62.8 yes View details
ndhF-rpl32 SSC 992 0.0072 0.99 62.2 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGAACTGTTCGGGATCTTT 789–812 1.000 69.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTGTTCGGGATCTTT 788–811 1.000 69.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC AGGAACTGTTCGGGATCTTT 804–827 1.000 69.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGGAACTGTTCGGGATCTTT 798–821 1.000 68.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTGTTCGGGATCTTTT 788–811 1.000 67.9
rps16_p1 rps16 TTTTGTTTGATTAGGACCAAG TGGGTTCCAAATTAGAGGAA 1141–1142 1.000 40.7
rps16_p2 rps16 TTTTGTTTGATTAGGACCAAG ATGGGTTCCAAATTAGAGGA 1142–1143 1.000 40.7
rps16_p3 rps16 ATTTTGTTTGATTAGGACCAAG TGGGTTCCAAATTAGAGGAA 1142–1143 1.000 40.7
rps16_p4 rps16 TTTTGTTTGATTAGGACCAAG ATGGGTTCCAAATTAGAGGAA 1142–1143 1.000 40.7
rps16_p5 rps16 TTTTGTTTGATTAGGACCAAG TGGGTTCCAAATTAGAGGAAT 1141–1142 1.000 40.7
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 212–220 1.000 67.1
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 215–223 1.000 66.8
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 218–226 1.000 66.3
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 221–229 1.000 66.0
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 216–224 1.000 64.6
atpA-atpF_p1 atpA-atpF CCGTCACCTACTTGCAGTAC AAGGGGCTCTAGGAACTCTG 260 1.000 79.5
atpA-atpF_p2 atpA-atpF CCGTCACCTACTTGCAGTAC CAAGGGGCTCTAGGAACTCT 261 1.000 79.5
atpA-atpF_p3 atpA-atpF GTCACCTACTTGCAGTACGG AAGGGGCTCTAGGAACTCTG 258 1.000 79.5
atpA-atpF_p4 atpA-atpF GTCACCTACTTGCAGTACGG CAAGGGGCTCTAGGAACTCT 259 1.000 79.5
atpA-atpF_p5 atpA-atpF GTCACCTACTTGCAGTACGG CCTTACAAGGGGCTCTAGGA 264 1.000 79.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 1166–1211 1.000 83.1
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 1222–1267 1.000 82.3
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 1182–1227 1.000 82.1
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 1167–1212 1.000 81.9
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 1226–1271 1.000 81.7
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATCC 1066–1325 1.000 78.8
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATCC 1005–1264 1.000 77.2
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT GCTACTGCACTGTTCATCCT 1065–1324 1.000 76.4
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT GCTACTGCACTGTTCATCCT 1004–1263 1.000 74.9
petN-psbM_p5 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATCC 1067–1326 1.000 72.9

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
Nothosmyrnium japonicum MT561036.1 140902 View on NCBI ↗
Nothosmyrnium xizangense var. simpliciorum PV794570.1 140701 View on NCBI ↗