Markers + reference

Ulmus

23 species · Ulmaceae · Rosales

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Species 23
Genome length 159–160 kb
Candidate markers 267
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1218 0.0342 0.83 69.6 yes View details
trnS-GCU-trnG-GCC LSC 940 0.0672 0.81 81.8 yes View details
trnT-GGU-psbD LSC 1207 0.0269 0.95 79.7 yes View details
rpl2 IRb 1510 0.0009 1.00 28.5 no View details
ndhF-rpl32 SSC 1126 0.0275 0.94 66.8 yes View details
rpl32-trnL-UAG SSC 1099 0.0342 0.95 74.4 yes View details
ndhA SSC 2555 0.0118 0.99 70.1 yes View details
rpl2 IRa 1510 0.0009 1.00 36.9 yes View details
rps19-trnH-GUG LSC 75 0.2349 0.99 76.6 no View details
trnH-GUG-psbA LSC 241 0.0581 0.85 67.8 yes View details
psbE-petL LSC 1390 0.0172 0.98 66.9 yes View details
psbI-trnS-GCU LSC 144 0.0257 1.00 66.8 yes View details
ndhC-trnV-UAC LSC 720 0.0219 0.94 65.9 yes View details
trnW-CCA-trnP-UGG LSC 169 0.0281 0.96 64.2 yes View details
rps2-rpoC2 LSC 215 0.0211 1.00 64.1 yes View details
trnR-UCU-atpA LSC 343 0.0222 0.88 62.9 yes View details
trnF-GAA-ndhJ LSC 723 0.0091 0.99 62.0 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA AATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 314–390 1.000 89.1
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 264–340 1.000 88.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 267–343 1.000 88.7
trnH-GUG-psbA_p4 trnH-GUG-psbA TTGCCTTAATCCACTTGGCT GCGCTAACCTTGGTATGGAA 321–397 1.000 86.9
trnH-GUG-psbA_p5 trnH-GUG-psbA TTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 271–347 1.000 86.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1078–1291 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 1108–1321 1.000 89.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1092–1305 1.000 88.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG TAAGGCATCGGGTTTTGGTC 1122–1335 1.000 87.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTAAGGCATCGGGTTTTGGT 1109–1322 1.000 87.2
psbI-trnS-GCU_p1 psbI-trnS-GCU ATGATCCGGGTCGTAATCCT TGGACTAAAGCGTCGGATTG 245–279 1.000 89.5
psbI-trnS-GCU_p2 psbI-trnS-GCU ATGATCCGGGTCGTAATCCT GTGGACTAAAGCGTCGGATT 246–280 1.000 89.4
psbI-trnS-GCU_p3 psbI-trnS-GCU ATGATCCGGGTCGTAATCCT GACTAAAGCGTCGGATTGCT 243–277 1.000 86.7
psbI-trnS-GCU_p4 psbI-trnS-GCU ATGATCCGGGTCGTAATCCT CTGAGTGGACTAAAGCGTCG 250–284 1.000 86.3
psbI-trnS-GCU_p5 psbI-trnS-GCU ATGATCCGGGTCGTAATCCT ATGGCTGAGTGGACTAAAGC 254–288 1.000 85.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TAATCAAACCGAGGGATCCC 905–1220 1.000 81.4
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TAATCAAACCGAGGGATCCC 904–1219 1.000 81.4
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA TAATCAAACCGAGGGATCCC 959–1274 1.000 80.3
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TTAATCAAACCGAGGGATCCC 906–1221 1.000 79.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TTAATCAAACCGAGGGATCCC 905–1220 1.000 79.4
trnR-UCU-atpA_p1 trnR-UCU-atpA ATGGAAATGAAAGGCGTCCA TCAGGAACAGATGGAACGTT 433–483 1.000 77.9
trnR-UCU-atpA_p2 trnR-UCU-atpA ATGGAAATGAAAGGCGTCCA TTCAGGAACAGATGGAACGT 434–484 1.000 77.9
trnR-UCU-atpA_p3 trnR-UCU-atpA TGGAAATGAAAGGCGTCCAT TCAGGAACAGATGGAACGTT 432–482 1.000 77.9
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAAATGAAAGGCGTCCAT TTCAGGAACAGATGGAACGT 433–483 1.000 77.9
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAAATGAAAGGCGTCCAT TCAGGAACAGATGGAACGTTT 432–482 1.000 75.8
rps2-rpoC2_p1 rps2-rpoC2 GGTGCCATTCTAGGATTCCA ACATCAGAACAATCATTTCTGGG 349–370 0.957 47.9
rps2-rpoC2_p2 rps2-rpoC2 ACTCCTGCTTCCATCATCTCT ACATCAGAACAATCATTTCTGGG 304–325 0.957 47.9
rps2-rpoC2_p3 rps2-rpoC2 TGAACTCCTGCTTCCATCATC ACATCAGAACAATCATTTCTGGG 307–328 0.957 47.8
rps2-rpoC2_p4 rps2-rpoC2 TGACCAAAATGAACTCCTGCT ACATCAGAACAATCATTTCTGGG 316–337 0.957 47.7
rps2-rpoC2_p5 rps2-rpoC2 GGTGCCATTCTAGGATTCCA CATCAGAACAATCATTTCTGGGA 348–369 0.957 47.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

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

Species Accession Length (bp) Link
Ulmus alata MT165919.1 159353 View on NCBI ↗
Ulmus bergmanniana NC_057601.1 160060 View on NCBI ↗
Ulmus canescens MT165922.1 159187 View on NCBI ↗
Ulmus castaneifolia NC_063958.1 159924 View on NCBI ↗
Ulmus changii MT742250.1 159832 View on NCBI ↗
Ulmus crassifolia MT165926.1 159338 View on NCBI ↗
Ulmus densa MT742251.1 159494 View on NCBI ↗
Ulmus elongata NC_046061.1 159230 View on NCBI ↗
Ulmus glabra MT165931.1 159305 View on NCBI ↗
Ulmus glaucescens MT165932.1 159342 View on NCBI ↗
Ulmus laevis NC_064394.1 159712 View on NCBI ↗
Ulmus lamellosa NC_063959.1 160388 View on NCBI ↗
Ulmus lanceifolia NC_058620.1 158652 View on NCBI ↗
Ulmus mianzhuensis NC_077557.1 159425 View on NCBI ↗
Ulmus microcarpa MT165938.1 159795 View on NCBI ↗
Ulmus minor MT165939.1 159304 View on NCBI ↗
Ulmus prunifolia MT165941.1 159712 View on NCBI ↗
Ulmus rubra MT165943.1 159202 View on NCBI ↗
Ulmus serotina MT165944.1 159270 View on NCBI ↗
Ulmus szechuanica MT165945.1 159588 View on NCBI ↗
Ulmus thomasii MT165946.1 159457 View on NCBI ↗
Ulmus uyematsui MT165947.1 159693 View on NCBI ↗
Ulmus wallichiana MT165948.1 159422 View on NCBI ↗