Markers + reference

Zelkova

4 species · Ulmaceae · Rosales

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Species 4
Genome length 159–159 kb
Candidate markers 267
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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 25.1 yes View details
matK-rps16 LSC 1825 0.0108 0.99 55.9 yes View details
trnS-GCU-trnG-GCC LSC 849 0.0250 0.94 74.0 yes View details
trnG-GCC-trnR-UCU LSC 372 0.0193 0.82 61.4 yes View details
atpF LSC 1296 0.0030 1.00 39.5 yes View details
trnT-GGU-psbD LSC 1185 0.0104 0.99 67.3 yes View details
psbZ-trnG-GCC LSC 431 0.0186 0.99 68.9 yes View details
ycf3 LSC 2062 0.0054 1.00 56.4 yes View details
ndhC-trnV-UAC LSC 754 0.0120 0.92 63.1 yes View details
trnP-UGG-psaJ LSC 393 0.0017 1.00 42.2 yes View details
ndhA SSC 2583 0.0121 0.99 52.9 yes View details
trnH-GUG-psbA LSC 198 0.0530 0.96 83.6 yes View details
trnW-CCA-trnP-UGG LSC 152 0.0526 1.00 66.1 yes View details
accD-psaI LSC 478 0.0087 1.00 65.3 yes View details
rpoB-trnC-GCA LSC 1346 0.0062 0.99 64.6 yes View details
rpl16 LSC 1500 0.0030 0.97 63.7 yes View details
rps11-rpl36 LSC 135 0.0160 1.00 63.4 yes View details
rps16-trnQ-UUG LSC 1085 0.0065 0.92 62.2 yes View details
rps18-rpl20 LSC 217 0.0061 0.99 61.7 yes View details
rps2-rpoC2 LSC 220 0.0076 0.98 60.9 yes View details
psbC LSC 1422 0.0029 1.00 60.7 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 AATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 264–323 1.000 83.9
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 267–326 1.000 83.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 314–373 1.000 83.1
trnH-GUG-psbA_p4 trnH-GUG-psbA TTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 271–330 1.000 81.5
trnH-GUG-psbA_p5 trnH-GUG-psbA TTGCCTTAATCCACTTGGCT GCGCTAACCTTGGTATGGAA 321–380 1.000 80.8
psbA_p1 psbA AATCCACTTGGCTACATCCG ATTCATGTGCTTGGGAGTCC 1337–1396 1.000 77.8
psbA_p2 psbA AATCCACTTGGCTACATCCG GAAAGCCGTGTGCAATGAAA 1705–1765 1.000 77.7
psbA_p3 psbA AATCCACTTGGCTACATCCG CGGCTTGGGGAGAGATTTTT 1675–1735 1.000 77.5
psbA_p4 psbA AATCCACTTGGCTACATCCG CTAGTTCCGGGTTCGAATCC 1593–1653 1.000 77.0
psbA_p5 psbA AATCCACTTGGCTACATCCG CTGTTGAATAACAAGCCCGC 1382–1441 1.000 76.8
matK-rps16_p1 matK-rps16 CCACGATCATGAGCAAATGC GCCGTACGAGGAGAAAACTT 2199–2255 1.000 82.5
matK-rps16_p2 matK-rps16 TGCAACGAAGAGGCATCTTT GCCGTACGAGGAGAAAACTT 2613–2669 1.000 82.2
matK-rps16_p3 matK-rps16 AATGCAACGAAGAGGCATCT GCCGTACGAGGAGAAAACTT 2615–2671 1.000 82.0
matK-rps16_p4 matK-rps16 CCACGATCATGAGCAAATGC TCGATCCCGAAGAGAAGGAA 2098–2157 1.000 82.0
matK-rps16_p5 matK-rps16 TGCAACGAAGAGGCATCTTT TCGATCCCGAAGAGAAGGAA 2512–2571 1.000 81.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1105–1175 1.000 83.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1088–1158 1.000 83.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TAAGGCATCGGGTTTTGGTC 1135–1205 1.000 82.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1106–1176 1.000 82.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 1118–1188 1.000 82.3
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TAATCAAACCGAGGGATCCC 871–1051 1.000 76.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TAATCAAACCGAGGGATCCC 870–1050 1.000 76.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA TAATCAAACCGAGGGATCCC 925–1105 1.000 74.9
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TTAATCAAACCGAGGGATCCC 872–1052 1.000 74.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TTAATCAAACCGAGGGATCCC 871–1051 1.000 74.2
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 380–485 1.000 69.4
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 383–488 1.000 69.1
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 386–491 1.000 68.7
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 389–494 1.000 68.4
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 384–489 1.000 66.9

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
Zelkova abelicea MT165949.1 158973 View on NCBI ↗
Zelkova carpinifolia MT165950.1 159026 View on NCBI ↗
Zelkova schneideriana NC_041074.1 158991 View on NCBI ↗
Zelkova sinica PV008712.1 158919 View on NCBI ↗