Markers + reference

Sternbergia

2 species · Amaryllidaceae · Asparagales

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Species 2
Genome length 158–159 kb
Candidate markers 271
Primer pairs 85

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 9 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 1258 0.0209 0.95 65.7 yes View details
atpF LSC 1582 0.0306 0.99 65.8 yes View details
rpl22 LSC 387 0.0388 1.00 76.6 yes View details
ndhF SSC 2223 0.0122 1.00 55.1 yes View details
ccsA SSC 966 0.0052 1.00 47.0 yes View details
psaC-ndhE SSC 479 0.0373 0.95 80.4 yes View details
ycf1 SSC 5460 0.0207 0.97 52.4 yes View details
ccsA-ndhD SSC 231 0.0736 1.00 84.2 yes View details
psbC-trnS-UGA LSC 127 0.0635 0.99 83.6 yes View details
psbA-trnK-UUU LSC 237 0.0295 1.00 63.7 yes View details
petN-psbM LSC 975 0.0114 0.99 63.1 yes View details
psbM-trnD-GUC LSC 1032 0.0111 0.96 62.8 yes View details
trnR-ACG-trnN-GUU IRb 602 0.0066 1.00 62.6 yes View details
trnN-GUU-trnR-ACG IRa 602 0.0066 1.00 62.6 yes View details
ndhJ-ndhK LSC 81 0.0247 1.00 61.2 yes View details
clpP-psbB LSC 435 0.0115 1.00 61.2 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU AAAACACCGAACCATCCGAT AAAATGCAAGCACGGTTTGG 448–449 1.000 76.3
psbA-trnK-UUU_p2 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT AAAATGCAAGCACGGTTTGG 427–428 1.000 76.0
psbA-trnK-UUU_p3 psbA-trnK-UUU AAAACACCGAACCATCCGAT CTTCATCCGACTAGTTCCGG 385–386 1.000 75.9
psbA-trnK-UUU_p4 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT AAAATGCAAGCACGGTTTGG 377–378 1.000 75.7
psbA-trnK-UUU_p5 psbA-trnK-UUU CACCGAACCATCCGATGTAA AAAATGCAAGCACGGTTTGG 444–445 1.000 75.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA CGAACGAATCACACTTTTACCA 1335–1345 1.000 63.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA TCGAACGAATCACACTTTTACC 1336–1346 1.000 61.1
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CGGAGAGAGAGGGATTCGAA CGAACGAATCACACTTTTACCA 1383–1393 1.000 60.8
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC GCTTTAGTCCACTCAGCCAT CGAACGAATCACACTTTTACCA 1321–1331 1.000 60.3
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AGTCCACTCAGCCATCTCTC CGAACGAATCACACTTTTACCA 1316–1326 1.000 59.5
atpF_p1 atpF TCGAAGAGTTACCATTAGTGTCTC AGCTCTGTTCTTTGTTAGTCCT 1716–1823 1.000 42.8
atpF_p2 atpF CGAAGAGTTACCATTAGTGTCTCT AGCTCTGTTCTTTGTTAGTCCT 1715–1822 1.000 42.8
atpF_p3 atpF TCGAAGAGTTACCATTAGTGTCT AGCTCTGTTCTTTGTTAGTCCT 1716–1823 1.000 42.8
atpF_p4 atpF TCGAAGAGTTACCATTAGTGTCTC AGAGCTCTGTTCTTTGTTAGTCC 1718–1825 1.000 42.8
atpF_p5 atpF TCGAAGAGTTACCATTAGTGTCTC GAGCTCTGTTCTTTGTTAGTCCT 1717–1824 1.000 42.8
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 1127–1130 1.000 70.0
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 1076–1079 1.000 69.2
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 1075–1078 1.000 69.2
petN-psbM_p4 petN-psbM ATGGTAAGTCTTGCTTGGGC TGCTACTGCACTGTTCATTCT 1135–1138 1.000 68.8
petN-psbM_p5 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTGTTCATTCT 1074–1077 1.000 68.7
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CCTCGCTGGGATTGTAGTTC 1128–1160 1.000 65.1
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC AGTTCAATCGGTCAGAGCAC 1113–1145 1.000 64.9
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TACACCTCGCTGGGATTGTA 1132–1164 1.000 64.4
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA CCTCGCTGGGATTGTAGTTC 1135–1167 1.000 61.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA AGTTCAATCGGTCAGAGCAC 1120–1152 1.000 61.7
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTGGCTGAGTGGTTGATAG 239–240 1.000 81.5
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 228–229 1.000 81.4
psbC-trnS-UGA_p3 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GCTGAGTGGTTGATAGCTCC 235–236 1.000 81.3
psbC-trnS-UGA_p4 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGCTGAGTGGTTGATAGCTC 236–237 1.000 81.3
psbC-trnS-UGA_p5 psbC-trnS-UGA TTCCATGACCCCTCTTAGCT GGTGGCTGAGTGGTTGATAG 231–232 1.000 80.7

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
Sternbergia candida PP853234.1 158073 View on NCBI ↗
Sternbergia lutea PP853235.1 158599 View on NCBI ↗