Markers + reference

Lycoris

21 species · Amaryllidaceae · Asparagales

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Species 21
Genome length 158–159 kb
Candidate markers 285
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 285 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 1205 0.0084 1.00 56.6 yes View details
atpF LSC 1480 0.0044 1.00 36.0 yes View details
ycf1 LSC 105 0.0000 1.00 19.4 no View details
psbZ-trnG-GCC LSC 331 0.0186 1.00 49.8 yes View details
trnT-UGU-trnL-UAA LSC 971 0.0080 0.99 52.1 yes View details
petA-psbJ LSC 1159 0.0061 1.00 45.8 yes View details
ycf1 IRb 948 0.0009 1.00 33.8 no View details
rpl32-trnL-UAG SSC 820 0.0094 1.00 44.6 yes View details
ndhD SSC 1506 0.0053 1.00 38.7 yes View details
psaC-ndhE SSC 438 0.0122 1.00 50.0 yes View details
rps15-ycf1 SSC 391 0.0100 0.99 49.5 yes View details
ycf1 SSC 5451 0.0050 1.00 34.7 yes View details
psbC-trnS-UGA LSC 146 0.0237 1.00 53.0 yes View details
ndhF-rpl32 SSC 935 0.0058 1.00 52.6 yes View details
rps16-trnQ-UUG LSC 1502 0.0038 1.00 49.1 yes View details
ycf1-trnD-GUC LSC 1048 0.0034 1.00 48.5 yes View details
ndhC-trnV-UAC LSC 1590 0.0036 1.00 48.0 yes View details
ycf3-trnS-GGA LSC 618 0.0011 1.00 47.3 yes View details
ndhA SSC 2223 0.0034 1.00 47.1 yes View details
clpP LSC 2058 0.0030 1.00 46.5 yes View details
psaA-ycf3 LSC 673 0.0067 1.00 45.4 yes View details
cemA LSC 726 0.0023 1.00 45.4 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1561–1576 1.000 80.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1572–1587 1.000 79.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1565–1580 1.000 75.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1591–1606 1.000 75.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1573–1588 1.000 75.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CGAACGAATCACACTTTTACCA 1266–1297 1.000 63.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TCGAACGAATCACACTTTTACC 1267–1298 1.000 61.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA CGAACGAATCACACTTTTACCA 1314–1345 1.000 60.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT CGAACGAATCACACTTTTACCA 1252–1283 1.000 60.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC CGAACGAATCACACTTTTACCA 1247–1278 1.000 59.5
atpF_p1 atpF CGCTCCTGGAAAGTAGTCAC CCGGGAAGGACTGATTTGAG 2537–2605 1.000 81.6
atpF_p2 atpF CGCTCCTGGAAAGTAGTCAC CGGGAAGGACTGATTTGAGG 2536–2604 1.000 81.6
atpF_p3 atpF CGCTCCTGGAAAGTAGTCAC CCTTCCCGTCCTTCGTTTAG 2502–2553 0.905 77.1
atpF_p4 atpF CCGAGATTCAGAAGCGGAAA CCTTCCCGTCCTTCGTTTAG 2239–2290 0.905 77.1
atpF_p5 atpF AAATAAGCCTCGCTCACTGG CCTTCCCGTCCTTCGTTTAG 2169–2220 0.905 76.9
ycf1-trnD-GUC_p1 ycf1-trnD-GUC AGAATGAACAGTGCAGTAGC GTATGCTATACACCTCGCCG 1151–1170 1.000 64.3
ycf1-trnD-GUC_p2 ycf1-trnD-GUC AGAATGAACAGTGCAGTAGC AGTTCAATCGGTCAGAGCAC 1124–1143 1.000 63.8
ycf1-trnD-GUC_p3 ycf1-trnD-GUC AGGAACTAGAATGAACAGTGCA GTATGCTATACACCTCGCCG 1158–1177 1.000 61.1
ycf1-trnD-GUC_p4 ycf1-trnD-GUC AGGAACTAGAATGAACAGTGCA AGTTCAATCGGTCAGAGCAC 1131–1150 1.000 60.6
ycf1-trnD-GUC_p5 ycf1-trnD-GUC GGAACTAGAATGAACAGTGCAG GTATGCTATACACCTCGCCG 1157–1176 1.000 58.6
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTGGCTGAGTGGTTGATAG 235–238 1.000 81.5
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GCTGAGTGGTTGATAGCTCC 231–234 1.000 81.4
psbC-trnS-UGA_p3 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGCTGAGTGGTTGATAGCTC 232–235 1.000 81.4
psbC-trnS-UGA_p4 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 224–227 1.000 81.4
psbC-trnS-UGA_p5 psbC-trnS-UGA TTCCATGACCCCTCTTAGCT GGTGGCTGAGTGGTTGATAG 227–230 1.000 80.7
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TGCTTCTTCTGATGGTTGGT GATCGAACCCGCATCTTCTC 474–476 1.000 71.1
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TGCTTCTTCTGATGGTTGGT GAACCCGCATCTTCTCCTTG 470–472 1.000 70.2
psbZ-trnG-GCC_p3 psbZ-trnG-GCC GCTTCTTCTGATGGTTGGTCA GATCGAACCCGCATCTTCTC 473–475 1.000 69.1
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TGCTTCTTCTGATGGTTGGTC GATCGAACCCGCATCTTCTC 474–476 1.000 69.1
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTGCTTCTTCTGATGGTTGGT GATCGAACCCGCATCTTCTC 475–477 1.000 69.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (21)

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

Species Accession Length (bp) Link
Lycoris anhuiensis NC_056294.1 158490 View on NCBI ↗
Lycoris aurea NC_046752.1 158690 View on NCBI ↗
Lycoris chinensis NC_047451.1 158473 View on NCBI ↗
Lycoris chunxiaoensis PX957146.2 158685 View on NCBI ↗
Lycoris flavescens NC_063555.1 158709 View on NCBI ↗
Lycoris haywardii NC_069836.1 158691 View on NCBI ↗
Lycoris houdyshelii NC_061747.1 158490 View on NCBI ↗
Lycoris hunanensis NC_081018.1 158415 View on NCBI ↗
Lycoris incarnata NC_061744.1 158405 View on NCBI ↗
Lycoris koreana NC_063563.1 158516 View on NCBI ↗
Lycoris longifolia NC_084293.1 158413 View on NCBI ↗
Lycoris longituba NC_047452.1 158633 View on NCBI ↗
Lycoris radiata NC_045077.1 158335 View on NCBI ↗
Lycoris rosea NC_061936.1 158723 View on NCBI ↗
Lycoris sanguinea NC_047453.1 158761 View on NCBI ↗
Lycoris shaanxiensis NC_061745.1 158498 View on NCBI ↗
Lycoris sprengeri NC_047454.1 158747 View on NCBI ↗
Lycoris squamigera NC_040164.1 158459 View on NCBI ↗
Lycoris straminea NC_061746.1 158490 View on NCBI ↗
Lycoris uydoensis NC_063557.1 158497 View on NCBI ↗
Lycoris x chejuensis NC_063556.1 158512 View on NCBI ↗