Markers + reference

Microtropis

2 species · Celastraceae · Celastrales

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Species 2
Genome length 157–157 kb
Candidate markers 273
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbI-trnS-GCU LSC 441 0.0898 0.93 82.7 yes View details
trnS-GCU-trnG-UCC LSC 930 0.0132 0.98 65.3 yes View details
trnG-UCC-trnR-UCU LSC 405 0.0167 0.89 65.5 yes View details
trnR-UCU-atpA LSC 290 0.0138 1.00 50.0 yes View details
rpoB-trnC-GCA LSC 1119 0.0108 0.99 59.6 yes View details
psbC-trnS-UGA LSC 253 0.0364 0.98 68.6 yes View details
trnT-UGU-trnL-UAA LSC 1131 0.0167 0.95 72.9 yes View details
rpl14 LSC 369 0.0081 1.00 44.6 yes View details
rpl16 LSC 1476 0.0069 0.98 56.4 yes View details
ccsA SSC 993 0.0050 1.00 49.4 yes View details
ccsA-ndhD SSC 212 0.0433 0.98 78.5 yes View details
ndhF-rpl32 SSC 605 0.0070 0.95 67.5 yes View details
trnM-CAU-atpE LSC 165 0.0242 1.00 66.4 yes View details
trnE-UUC-trnT-GGU LSC 712 0.0047 0.90 64.9 yes View details
petN-psbM LSC 1163 0.0062 0.97 64.8 yes View details
trnR-ACG-trnN-GUU IRb 616 0.0066 0.99 63.8 yes View details
trnN-GUU-trnR-ACG IRa 616 0.0066 0.99 63.8 yes View details
atpH-atpI LSC 1235 0.0057 0.99 62.6 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
psbI-trnS-GCU_p1 psbI-trnS-GCU GAAATCCCGGACGTGAAGAA GTTCTTCGTACCGAGGGTTC 474–501 1.000 89.3
psbI-trnS-GCU_p2 psbI-trnS-GCU GAAATCCCGGACGTGAAGAA TGAGTGGATTAAAGCGTCGG 514–541 1.000 88.9
psbI-trnS-GCU_p3 psbI-trnS-GCU GAAATCCCGGACGTGAAGAA ATTGGGAGAGATGGCTGAGT 529–556 1.000 87.9
psbI-trnS-GCU_p4 psbI-trnS-GCU GAAATCCCGGACGTGAAGAA GGCTGAGTGGATTAAAGCGT 517–544 1.000 86.8
psbI-trnS-GCU_p5 psbI-trnS-GCU GAAATCCCGGACGTGAAGAA TGGCTGAGTGGATTAAAGCG 518–545 1.000 86.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TCAAGGGGATCACTAGAACGA 1005–1012 1.000 74.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GCAACGGAAAGAGAGGGATT TCAAGGGGATCACTAGAACGA 1066–1073 1.000 72.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TCAAGGGGATCACTAGAACGA 1063–1070 1.000 72.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATCAACGCAACGGAAAGAGA TCAAGGGGATCACTAGAACGA 1072–1079 1.000 72.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CCAAGTTATCAACGCAACGG TCAAGGGGATCACTAGAACGA 1079–1086 1.000 71.9
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG ATAAATTGCGTCCATGCGTC 496–535 1.000 78.6
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG ATAAATTGCGTCCATGCGTC 499–538 1.000 78.4
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC ATAAATTGCGTCCATGCGTC 500–539 1.000 76.2
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AATAAATTGCGTCCATGCGTC 497–536 1.000 76.2
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AATAAATTGCGTCCATGCGTC 500–539 1.000 75.9
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG TGGAACGTTTTCTACTTCAGGA 405–415 1.000 46.8
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT TGGAACGTTTTCTACTTCAGGA 404–414 1.000 46.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACGTTTTCTACTTCAGGA 344–354 1.000 46.0
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG ACGTTTTCTACTTCAGGAACAGT 401–411 1.000 44.0
trnR-UCU-atpA_p5 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT ACGTTTTCTACTTCAGGAACAGT 400–410 1.000 44.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCCGCAG 1322–1332 1.000 79.5
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1292–1302 1.000 79.1
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCCGCAG 1323–1333 1.000 78.3
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 1293–1303 1.000 78.0
atpH-atpI_p5 atpH-atpI ATAGAAGCAAGACCGACAGC TTTTGCAACTTTAGCCGCAG 1355–1365 1.000 77.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1196–1207 1.000 80.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCCCTCATTTCCATCCCC TATGTTGATCAGGCGACACC 1215–1226 1.000 78.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGTTCCCTCATTTCCATCCC CCGGATTTGAACTGGGGAAA 1197–1208 1.000 78.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCCCTCATTTCCATCCCC AAAAGGATTTGCAGTCCCCC 1178–1189 1.000 78.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ACGTTCCCTCATTTCCATCC CCGGATTTGAACTGGGGAAA 1198–1209 1.000 77.5

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
Microtropis henryi NC_065709.1 157235 View on NCBI ↗
Microtropis osmanthoides NC_065714.1 156659 View on NCBI ↗