Markers + reference

Nasa

2 species · Loasaceae · Cornales

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Species 2
Genome length 158–158 kb
Candidate markers 270
Primer pairs 95

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 10 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 777 0.0622 0.93 80.4 yes View details
trnT-UGU-trnL-UAA LSC 700 0.0773 1.00 82.0 yes View details
ndhC-trnV-UAC LSC 1131 0.0591 0.94 79.9 yes View details
accD-psaI LSC 598 0.0781 0.86 77.0 yes View details
ycf4-cemA LSC 481 0.0850 0.95 83.2 yes View details
petA-psbJ LSC 1036 0.0779 0.71 71.1 yes View details
ycf1 IRb 971 0.0093 0.99 52.7 no View details
ndhF-rpl32 SSC 1039 0.0784 0.98 78.3 yes View details
rpl32-trnL-UAG SSC 799 0.0748 0.99 77.8 yes View details
ycf1 SSC 5715 0.0546 0.95 73.0 yes View details
petN-psbM LSC 1122 0.0490 1.00 86.6 yes View details
trnR-UCU-atpA LSC 131 0.1200 0.95 81.4 yes View details
rps16-trnQ-UUG LSC 1605 0.0576 0.97 81.3 yes View details
trnL-UAA-trnF-GAA LSC 363 0.0697 0.91 78.6 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0847 1.00 78.2 yes View details
trnW-CCA-trnP-UGG LSC 164 0.0513 0.95 78.2 yes View details
trnK-UUU-rps16 LSC 856 0.0509 0.94 77.3 yes View details
psbE-petL LSC 1310 0.0472 0.97 77.3 yes View details
trnH-GUG-psbA LSC 327 0.0801 0.95 77.2 yes View details
trnE-UUC-trnT-GGU LSC 726 0.0448 0.98 76.6 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 95 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 TGAAGCTCCATCTACAAATGG 374–378 1.000 60.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TGAAGCTCCATCTACAAATGG 388–392 1.000 60.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TGAAGCTCCATCTACAAATGG 387–391 1.000 60.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TGAAGCTCCATCTACAAATGG 389–393 1.000 60.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTGAAGCTCCATCTACAAATGG 375–379 1.000 58.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GCCGTACGAGGAGAAAACTT 1257–1280 1.000 85.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1256–1279 1.000 85.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG TCATTTTTGCTCGAGCCGTA 1271–1294 1.000 85.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCATTTTTGCTCGAGCCGTA 1270–1293 1.000 85.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGACCCAAACTCGTTTTGT GCCGTACGAGGAGAAAACTT 1381–1400 1.000 84.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1695–1724 1.000 85.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1678–1707 1.000 84.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1696–1725 1.000 83.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1693–1722 1.000 82.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1692–1721 1.000 82.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 846–854 1.000 59.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 845–853 1.000 59.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CCATCAACGGAAAGAGAGGG ACGAATCACACTTTTACCACT 906–914 1.000 59.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 900–908 1.000 58.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACGAATCACACTTTTACCACT 847–855 1.000 58.0
trnR-UCU-atpA_p1 trnR-UCU-atpA ATCGGAATCAAAAGCGTCCA CAGGAACAGATGGAGCGTTT 254–258 1.000 84.2
trnR-UCU-atpA_p2 trnR-UCU-atpA TCGGAATCAAAAGCGTCCAT CAGGAACAGATGGAGCGTTT 253–257 1.000 84.2
trnR-UCU-atpA_p3 trnR-UCU-atpA TCGGAATCAAAAGCGTCCAT ATTCAGGAACAGATGGAGCG 256–260 1.000 83.1
trnR-UCU-atpA_p4 trnR-UCU-atpA ATCGGAATCAAAAGCGTCCA ATTCAGGAACAGATGGAGCG 257–261 1.000 83.0
trnR-UCU-atpA_p5 trnR-UCU-atpA TCGGAATCAAAAGCGTCCAT AGGAACAGATGGAGCGTTTT 252–256 1.000 81.2
petN-psbM_p1 petN-psbM ACATTTTCCCTTTCGCTCGT TGCTACTGCACTGTTCATTCT 1246–1263 1.000 71.4
petN-psbM_p2 petN-psbM CCCTTTCGCTCGTAGTATGG TGCTACTGCACTGTTCATTCT 1239–1256 1.000 71.2
petN-psbM_p3 petN-psbM CCTTTCGCTCGTAGTATGGG TGCTACTGCACTGTTCATTCT 1238–1255 1.000 71.2
petN-psbM_p4 petN-psbM CTTTCGCTCGTAGTATGGGG TGCTACTGCACTGTTCATTCT 1237–1254 1.000 71.2
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1284–1301 1.000 70.9

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
Nasa triphylla NC_044802.1 157596 View on NCBI ↗
Nasa urens NC_044839.1 158122 View on NCBI ↗