Markers + reference

Nyssa

3 species · Nyssaceae · Cornales

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Species 3
Genome length 157–157 kb
Candidate markers 270
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 807 0.0017 0.99 55.1 yes View details
rpoC1 LSC 2807 0.0009 1.00 44.1 yes View details
trnC-GCA-petN LSC 815 0.0016 1.00 47.3 yes View details
petN-psbM LSC 1126 0.0018 1.00 59.9 yes View details
psbD LSC 1062 0.0013 1.00 47.1 yes View details
trnF-GAA-ndhJ LSC 676 0.0020 1.00 47.5 yes View details
rbcL LSC 1428 0.0019 1.00 47.4 yes View details
ndhB IRb 2212 0.0000 1.00 38.5 no View details
ndhI SSC 537 0.0025 1.00 36.5 yes View details
ycf1-trnN-GUU IRa 322 0.0000 1.00 26.0 yes View details
trnN-GUU-trnR-ACG IRa 593 0.0045 1.00 49.0 yes View details
ndhB IRa 2212 0.0015 1.00 45.7 yes View details
ycf3-trnS-GGA LSC 866 0.0015 1.00 59.7 yes View details
psbE-petL LSC 1289 0.0016 1.00 59.7 yes View details
rpoB-trnC-GCA LSC 1174 0.0011 1.00 59.5 yes View details
clpP LSC 2049 0.0007 1.00 58.1 yes View details
ycf4-cemA LSC 915 0.0015 1.00 57.7 yes View details
ndhF SSC 2235 0.0006 1.00 57.6 yes View details
rps2-rpoC2 LSC 218 0.0061 1.00 56.9 yes View details
rpoC2 LSC 4167 0.0005 1.00 53.2 yes View details
ycf3 LSC 1963 0.0000 1.00 52.5 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGTCCGTGTCAACCAATATCT TCTGATTTTATCTACACACCCT 2715–2717 1.000 40.1
trnK-UUU_p2 trnK-UUU TGTCCGTGTCAACCAATATCT TCTGATTTTATCTACACACCCTT 2715–2717 1.000 40.1
trnK-UUU_p3 trnK-UUU TGTCCGTGTCAACCAATATCT TTCTGATTTTATCTACACACCCT 2716–2718 1.000 40.1
trnK-UUU_p4 trnK-UUU TGTCCGTGTCAACCAATATCT TCTGATTTTATCTACACACCCTTT 2715–2717 1.000 40.1
trnK-UUU_p5 trnK-UUU TGTCCGTGTCAACCAATATCT TTCTGATTTTATCTACACACCCTT 2716–2718 1.000 40.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAATCAAACCAAAAGACCCCT 912–921 1.000 64.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAATCAAACCAAAAGACCCCT 911–920 1.000 64.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATCAAACCAAAAGACCCCT 966–975 1.000 63.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAATCAAACCAAAAGACCCC 912–921 1.000 61.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAATCAAACCAAAAGACCCC 911–920 1.000 61.8
rps2-rpoC2_p1 rps2-rpoC2 AACTCCTGCCTCCATCATCT TTTTGTTCCACCACCGAAAA 366–367 1.000 66.1
rps2-rpoC2_p2 rps2-rpoC2 TGCCTCCATCATCTCTTCCA TTTTGTTCCACCACCGAAAA 360–361 1.000 66.0
rps2-rpoC2_p3 rps2-rpoC2 TCCTGCCTCCATCATCTCTT TTTTGTTCCACCACCGAAAA 363–364 1.000 65.5
rps2-rpoC2_p4 rps2-rpoC2 GAACTCCTGCCTCCATCATC TTTTGTTCCACCACCGAAAA 367–368 1.000 64.9
rps2-rpoC2_p5 rps2-rpoC2 CTCCTGCCTCCATCATCTCT TTTTGTTCCACCACCGAAAA 364–365 1.000 64.7
rpoC2_p1 rpoC2 CCCGATGGGTCATTCCTTTT GCAAACCAATTCGGGGAATT 214 1.000 73.1
rpoC2_p2 rpoC2 CCCGATGGGTCATTCCTTTT GCAAACCAATTCGGGGAATTT 214 1.000 70.8
rpoC2_p3 rpoC2 CCCGATGGGTCATTCCTTTT GGCAAACCAATTCGGGGAAT 215 1.000 70.4
rpoC2_p4 rpoC2 TGCGATCTGACCCATTTTCA GCAAACCAATTCGGGGAATT 249 1.000 70.3
rpoC2_p5 rpoC2 GGTGCGATCTGACCCATTTT GCAAACCAATTCGGGGAATT 251 1.000 69.9
rpoC1_p1 rpoC1 TGAACCGGAGAGACCTGAAT TTGCTCGTTCGAGAACTACG 2974 1.000 79.3
rpoC1_p2 rpoC1 TGAACCGGAGAGACCTGAAT ACGATCTTTGGCTCTGGAAC 2957 1.000 78.8
rpoC1_p3 rpoC1 AGACCTGAATTCCCACTGGT TTGCTCGTTCGAGAACTACG 2964 1.000 77.8
rpoC1_p4 rpoC1 TTGAACCGGAGAGACCTGAA TTGCTCGTTCGAGAACTACG 2975 1.000 77.5
rpoC1_p5 rpoC1 AGACCTGAATTCCCACTGGT ACGATCTTTGGCTCTGGAAC 2947 1.000 77.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTGA CCGGATTTGAACTGGGGAAA 1339–1340 1.000 77.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AGTTCTTCCGTCAAACCCTG CCGGATTTGAACTGGGGAAA 1340–1341 1.000 77.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CTTCCGTCAAACCCTGATCA CCGGATTTGAACTGGGGAAA 1336–1337 1.000 75.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTGA AAAAGGATTTGCAGTCCCCC 1321–1322 1.000 75.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AGTTCTTCCGTCAAACCCTG AAAAGGATTTGCAGTCCCCC 1322–1323 1.000 75.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Nyssa ogeche NC_044828.1 156586 View on NCBI ↗
Nyssa sinensis PP078668.1 156585 View on NCBI ↗
Nyssa wenshanensis MG524995.1 156598 View on NCBI ↗