Markers + reference

Kitagawia

6 species · Apiaceae · Apiales

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Species 6
Genome length 147–148 kb
Candidate markers 264
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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0040 1.00 27.7 yes View details
rps16-trnQ-UUG LSC 1258 0.0119 0.98 49.4 yes View details
rpoB-trnC-GCA LSC 1215 0.0139 0.99 51.7 yes View details
ycf2 LSC 6264 0.0088 1.00 44.5 yes View details
ycf2-trnL-CAA IRb 1407 0.0735 0.92 82.0 yes View details
ycf1 IRb 1884 0.0021 1.00 42.4 no View details
ndhF-rpl32 SSC 1036 0.0174 0.98 62.2 yes View details
rpl32-trnL-UAG SSC 968 0.0249 0.98 65.9 yes View details
ycf1 SSC 5487 0.0079 1.00 45.0 yes View details
trnL-CAA-trnH-GUG IRa 1368 0.0762 0.97 83.2 no View details
trnH-GUG-psbA LSC 204 0.0490 0.90 81.4 yes View details
trnT-GGU-psbD LSC 1428 0.0084 1.00 69.7 yes View details
psaA-ycf3 LSC 746 0.0089 0.95 61.5 yes View details
psbM-trnD-GUC LSC 689 0.0133 1.00 61.2 yes View details
rpl20-rps12 LSC 790 0.0062 0.98 60.3 yes View details
ndhC-trnV-UAC LSC 1114 0.0116 0.98 57.0 yes View details
trnS-GCU-trnG-UCC LSC 554 0.0132 1.00 56.3 yes View details
trnG-UCC-trnR-UCU LSC 144 0.0190 0.97 53.9 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 257–273 1.000 89.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 271–287 1.000 88.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 270–286 1.000 88.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 272–288 1.000 88.6
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGGAAGTTATGCACGAACGT 292–308 1.000 87.5
psbA_p1 psbA ACTCGTATATACTAAAACCCGGT AAATTCGTGTGCTTGGGAGT 1137 1.000 45.5
psbA_p2 psbA ACTCGTATATACTAAAACCCGGT TGCTTGGGAGTCCCTGATAA 1128 1.000 45.4
psbA_p3 psbA AACTCGTATATACTAAAACCCGGT AAATTCGTGTGCTTGGGAGT 1138 1.000 42.8
psbA_p4 psbA ACTCGTATATACTAAAACCCGGTC AAATTCGTGTGCTTGGGAGT 1137 0.833 39.2
psbA_p5 psbA ACTCGTATATACTAAAACCCGGTC TGCTTGGGAGTCCCTGATAA 1128 0.833 39.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT TGGAAGTATAGATGGGGCGT 1361–1380 1.000 83.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT TGGAAGTATAGATGGGGCGT 1362–1381 1.000 83.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT CTTACAGCAGCTTGCCAAAC 1875–1894 1.000 82.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT CTTACAGCAGCTTGCCAAAC 1876–1895 1.000 82.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GATTCCCGCGTGATACACTT CTTACAGCAGCTTGCCAAAC 2232–2251 1.000 82.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GGGGGTTACTCGAACGAATC 640–658 1.000 81.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TAAGGGGGTTACTCGAACGA 643–661 1.000 80.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGGGGGTTACTCGAACGAAT 641–659 1.000 78.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GGGGGTTACTCGAACGAATC 626–644 1.000 78.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGGGGTTACTCGAACGAATC 621–639 1.000 77.5
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 209–224 1.000 69.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 212–227 1.000 68.9
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 215–230 1.000 68.5
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 218–233 1.000 68.2
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 213–228 1.000 66.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT CCGGATTTGAACTGGGGAAA 1356–1372 1.000 81.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCACGAACCTACAAAAGCC CCGGATTTGAACTGGGGAAA 1357–1373 1.000 81.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT TTATTGATCAGGCGACACCC 1374–1390 1.000 79.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCACGAACCTACAAAAGCC TTATTGATCAGGCGACACCC 1375–1391 1.000 79.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT AAAAGGATTTGCAGTCCCCC 1338–1354 1.000 78.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Kitagawia baicalensis NC_070403.1 147985 View on NCBI ↗
Kitagawia formosana NC_070399.1 146999 View on NCBI ↗
Kitagawia praeruptora NC_060841.1 146930 View on NCBI ↗
Kitagawia stepposa NC_070402.1 147965 View on NCBI ↗
Kitagawia terebinthacea NC_070400.1 148327 View on NCBI ↗
Kitagawia terebinthacea var. terebinthacea PX549446.1 147733 View on NCBI ↗