Markers + reference

Morina

7 species · Caprifoliaceae · Dipsacales

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Species 7
Genome length 149–158 kb
Candidate markers 263
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 357 0.1168 0.46 69.8 yes View details
trnE-UUC-trnT-GGU LSC 927 0.0818 0.54 72.6 yes View details
ycf3 LSC 2039 0.0758 0.61 67.3 yes View details
ycf3-trnS-GGA LSC 315 0.0895 0.97 72.8 yes View details
ndhC-trnV-UAC LSC 1042 0.0787 0.88 82.2 yes View details
accD LSC 2205 0.0655 0.80 71.1 yes View details
ycf2-trnL-CAA IRb 704 0.1266 0.37 66.6 yes View details
trnR-ACG-trnN-GUU IRb 778 0.0836 0.66 76.2 yes View details
trnN-GUU-ndhF SSC 789 0.1569 0.99 73.7 yes View details
ycf1-trnN-GUU SSC 474 0.1567 0.97 66.0 yes View details
trnN-GUU-trnR-ACG IRa 778 0.0819 0.66 76.2 yes View details
trnL-CAA-ycf2 IRa 704 0.1242 0.35 66.4 yes View details
trnI-CAU-trnH-GUG LSC 731 0.1075 0.42 77.3 no View details
trnK-UUU-rps16 LSC 609 0.0663 0.93 84.8 yes View details
rps18 LSC 640 0.0872 0.86 80.1 yes View details
rps3 LSC 731 0.0520 0.89 76.5 yes View details
rps16-trnQ-UUG LSC 1817 0.0392 0.93 74.8 yes View details
trnS-GCU-trnG-GCC LSC 775 0.0371 0.97 72.5 yes View details
rpoB-trnC-GCA LSC 1246 0.0266 0.95 68.9 yes View details
rpl32-trnL-UAG SSC 829 0.0335 0.86 68.6 yes View details
psbE-petL LSC 1336 0.0237 0.98 66.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CAAGAGAAGTATGTAGATTACTAAA CGGATGTAGCCAAGTGGATC 199 0.143 5.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAAGAGAAGTATGTAGATTACTAAA CTTCTCTTGGGCGGATGTAG 210 0.143 5.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CAAGAGAAGTATGTAGATTACTAAA ACATACTTCTCTTGGGCGGA 215 0.143 5.7
trnH-GUG-psbA_p4 trnH-GUG-psbA CAAGAGAAGTATGTAGATTACTAAA ACTTCTCTTGGGCGGATGTA 211 0.143 5.7
trnH-GUG-psbA_p5 trnH-GUG-psbA CAAGAGAAGTATGTAGATTACTAAA TACTTCTCTTGGGCGGATGT 212 0.143 5.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GAACTTCGCCCCAATCAAAC 499–679 1.000 87.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GAACTTCGCCCCAATCAAAC 498–678 1.000 87.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GAACTTCGCCCCAATCAAAC 485–665 1.000 85.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCCCCAATCAAACGCAATTA 492–672 1.000 85.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCCCCAATCAAACGCAATTA 491–671 1.000 85.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TCGGAGGTTCGAATCCTTTC 1539–1893 1.000 85.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1566–1920 1.000 85.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGCTATTC 1557–1911 1.000 83.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTAAGGCAACGGGTTTTGGT 1567–1921 1.000 83.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTGGTAAGGCAACGGGTTTT 1570–1924 1.000 83.2
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AGGGGCTTAATAGAACGAATCA 834–861 0.286 29.4
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GGGGCTTAATAGAACGAATCAC 833–860 0.286 29.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA AGGGGCTTAATAGAACGAATCA 847–874 0.286 29.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA GGGGCTTAATAGAACGAATCAC 846–873 0.286 28.8
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA AGGGGCTTAATAGAACGAATCA 883–910 0.286 28.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCCTCATTTCCATCCTGGA CCGGATTTGAACTGGGGAAA 1293–1332 1.000 85.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTCCCTCATTTCCATCCTGG CCGGATTTGAACTGGGGAAA 1294–1333 1.000 84.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTCCATCCTGGA AAAAGGATTTGCAGTCCCCC 1275–1314 1.000 83.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTCCCTCATTTCCATCCTGG AAAAGGATTTGCAGTCCCCC 1276–1315 1.000 82.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCCCTCATTTCCATCCTGGA GTCTTTTGTTGATCAGGCGG 1316–1355 1.000 81.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AACTTCCTTTCGCAGTACCC GAACCGATGACTTACGCCTT 665–1075 1.000 90.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 620–1030 1.000 89.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 599–1009 1.000 89.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AACTTCCTTTCGCAGTACCC CCGATGACTTACGCCTTACC 662–1072 1.000 89.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCGATGACTTACGCCTTACC 617–1027 1.000 88.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Morina alba NC_045055.1 157999 View on NCBI ↗
Morina chinensis ON357685.1 154914 View on NCBI ↗
Morina chlorantha MK443504.1 154669 View on NCBI ↗
Morina kokonorica PQ722560.1 155035 View on NCBI ↗
Morina longifolia NC_045046.1 157149 View on NCBI ↗
Morina nepalensis NC_080497.1 155047 View on NCBI ↗
Morina nepalensis subsp. delavayi OK323964.1 149253 View on NCBI ↗