Markers + reference

Narcissus

7 species · Amaryllidaceae · Asparagales

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Species 7
Genome length 159–160 kb
Candidate markers 271
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 1264 0.0416 0.98 83.6 yes View details
atpF LSC 1505 0.0200 0.98 64.6 yes View details
trnC-GCA-petN LSC 1061 0.0268 1.00 71.6 yes View details
trnT-UGU-trnL-UAA LSC 1001 0.0357 0.99 76.9 yes View details
atpB-rbcL LSC 918 0.0261 1.00 71.1 yes View details
ndhF SSC 2214 0.0154 1.00 54.4 yes View details
ycf1 IRa 5349 0.0224 1.00 55.9 yes View details
rps19-psbA LSC 131 0.0428 0.96 73.5 no View details
rpoB-trnC-GCA LSC 1245 0.0237 0.98 71.2 yes View details
rpl22-rps19 IRb 54 0.0476 1.00 70.8 yes View details
rpl32-trnL-UAG SSC 785 0.0246 0.99 69.5 yes View details
petN-psbM LSC 860 0.0217 1.00 69.2 yes View details
atpF-atpH LSC 496 0.0289 1.00 67.8 yes View details
psbC-trnS-UGA LSC 127 0.0457 1.00 66.7 yes View details
trnT-GGU-psbD LSC 1085 0.0184 0.99 66.2 yes View details
ndhF-rpl32 SSC 923 0.0242 0.98 65.8 yes View details
ccsA-ndhD SSC 193 0.0449 1.00 65.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA CGAACGAATCACACTTTTACCA 1237–1341 1.000 69.5
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA TCGAACGAATCACACTTTTACC 1238–1342 1.000 67.5
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTTTAGTCCACTCAGCCAT CGAACGAATCACACTTTTACCA 1223–1327 1.000 66.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGTCCACTCAGCCATCTCTC CGAACGAATCACACTTTTACCA 1218–1322 1.000 65.8
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GATTCGAACCCTCGGTACAA CGAACGAATCACACTTTTACCA 1273–1377 1.000 64.3
atpF_p1 atpF CCGAGATTCAGAAGCGGAAA GGGCTGATTTGAGGATGAGG 2223–2319 1.000 87.1
atpF_p2 atpF CCGAGATTCAGAAGCGGAAA CTCGTTGCCATTTGCTTCTG 2303–2400 1.000 87.1
atpF_p3 atpF CCGAGATTCAGAAGCGGAAA ATTTATGGACTGGTCGTGGC 2427–2524 1.000 87.1
atpF_p4 atpF AAATAAGCCTCGCTCACTGG GGGCTGATTTGAGGATGAGG 2153–2249 0.857 81.2
atpF_p5 atpF CCAAATAAGCCTCGCTCACT GGGCTGATTTGAGGATGAGG 2155–2251 0.857 81.2
atpF-atpH_p1 atpF-atpH CATATTGTGCCCGGACTTCA ATTTATGGACTGGTCGTGGC 1041–1122 0.857 82.8
atpF-atpH_p2 atpF-atpH CATATTGTGCCCGGACTTCA AAGCCGTAGAAGGTATTGCG 1133–1214 0.857 82.2
atpF-atpH_p3 atpF-atpH CATATTGTGCCCGGACTTCA CAATATAAAATGCGCGCGGT 1458–1555 0.857 81.7
atpF-atpH_p4 atpF-atpH CATATTGTGCCCGGACTTCA CCAATTGAGGCAATGCATGG 1685–1800 0.857 81.6
atpF-atpH_p5 atpF-atpH CATATTGTGCCCGGACTTCA CCCAATTGAGGCAATGCATG 1686–1801 0.857 81.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA TAAAGGATTTGCAGTCCCCC 1283–1313 1.000 79.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCCCTCATTTCCATTCCGG TAAAGGATTTGCAGTCCCCC 1284–1314 1.000 79.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA TTTGTTGATCAGGCGACACC 1320–1350 1.000 77.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCCCTCATTTCCATTCCGG TTTGTTGATCAGGCGACACC 1321–1351 1.000 77.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA GACACCCGGATTTGAACTGG 1306–1336 1.000 76.9
trnC-GCA-petN_p1 trnC-GCA-petN GGGGGACTGCAAATCCTTTA CAGCCCAAGCAAGACTTACT 1100–1146 1.000 82.5
trnC-GCA-petN_p2 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC CAGCCCAAGCAAGACTTACT 1077–1123 1.000 80.2
trnC-GCA-petN_p3 trnC-GCA-petN TATCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 1082–1128 1.000 78.6
trnC-GCA-petN_p4 trnC-GCA-petN AATTTATTTGGCGGCATGGC CAGCCCAAGCAAGACTTACT 1169 0.143 43.8
trnC-GCA-petN_p5 trnC-GCA-petN AATTTATTTGGCGGCATGGC GCAGCCCAAGCAAGACTTA 1170 0.143 36.9
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC AAAACAGTCAGCCAAAATGA 909–1019 1.000 52.8
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT AAAACAGTCAGCCAAAATGA 908–1018 1.000 52.8
petN-psbM_p3 petN-psbM TATGGGGAAGGAGTGGACTC AAAACAGTCAGCCAAAATGA 907–1017 1.000 52.4
petN-psbM_p4 petN-psbM AGTATGGGGAAGGAGTGGAC TGTAAAAACAGTCAGCCAAAATGA 913–1023 1.000 52.0
petN-psbM_p5 petN-psbM GTATGGGGAAGGAGTGGACT TGTAAAAACAGTCAGCCAAAATGA 912–1022 1.000 52.0

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
Narcissus asturiensis PP853188.1 159693 View on NCBI ↗
Narcissus fernandesii PP853221.1 159213 View on NCBI ↗
Narcissus hybrid cultivar MW672399.1 159988 View on NCBI ↗
Narcissus papyraceus subsp. panizzianus PP853229.1 159843 View on NCBI ↗
Narcissus poeticus NC_039825.1 160099 View on NCBI ↗
Narcissus pseudonarcissus PP313599.1 160008 View on NCBI ↗
Narcissus tazetta subsp. chinensis MW322827.1 159376 View on NCBI ↗