Markers + reference

Galanthus

4 species · Amaryllidaceae · Asparagales

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Species 4
Genome length 156–158 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

8 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 1315 0.0111 0.90 60.8 yes View details
atpF-atpH LSC 490 0.0207 1.00 58.7 yes View details
trnT-UGU-trnL-UAA LSC 973 0.0099 0.88 49.2 yes View details
trnL-UAA-trnF-GAA LSC 364 0.0156 1.00 59.2 yes View details
atpB-rbcL LSC 940 0.0092 0.96 68.0 yes View details
petA-psbJ LSC 1134 0.0100 1.00 66.4 yes View details
ndhF SSC 2202 0.0065 1.00 46.7 yes View details
ycf1 SSC 5349 0.0090 1.00 59.2 yes View details
psbC-trnS-UGA LSC 127 0.0381 0.96 71.0 yes View details
petG-trnW-CCA LSC 114 0.0336 1.00 68.5 yes View details
rpoB-trnC-GCA LSC 1227 0.0084 1.00 66.0 yes View details
psbE-petL LSC 803 0.0025 1.00 65.3 yes View details
psaA-ycf3 LSC 645 0.0073 1.00 64.2 yes View details
petN-psbM LSC 961 0.0057 1.00 63.0 yes View details
rps19-psbA LSC 154 0.0227 1.00 61.4 no View details
psbB-psbT LSC 190 0.0115 0.99 61.3 yes View details
petD-rpoA LSC 153 0.0276 0.94 60.1 yes View details
rps2-rpoC2 LSC 165 0.0295 0.99 59.7 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
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CTCGTCCAACGGATTAGCAA CGAACGAATCACACTTTTACCA 1253–1428 1.000 63.5
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AACTCGTCCAACGGATTAGC CGAACGAATCACACTTTTACCA 1255–1430 1.000 63.5
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA CGAACGAATCACACTTTTACCA 1241–1416 1.000 63.3
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CTCGTCCAACGGATTAGCAA TCGAACGAATCACACTTTTACC 1254–1429 1.000 61.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AACTCGTCCAACGGATTAGC TCGAACGAATCACACTTTTACC 1256–1431 1.000 61.4
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG AGCGCTTTTATTTGCAAATCCT 588–591 1.000 64.4
atpF-atpH_p2 atpF-atpH CAGTGGCCTAAGGAAACGAA AGCGCTTTTATTTGCAAATCCT 560–563 1.000 64.0
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCATTAGCGCTTTTATTTGCA 593–596 1.000 61.6
atpF-atpH_p4 atpF-atpH CAGTGGCCTAAGGAAACGAA GCATTAGCGCTTTTATTTGCA 565–568 1.000 61.3
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG GCGCTTTTATTTGCAAATCCT 587–590 1.000 60.9
rps2-rpoC2_p1 rps2-rpoC2 GAGCCCTTATTGCAGCTGAT GAAGGTTGGAACGAGCGTAT 1099–1104 1.000 80.9
rps2-rpoC2_p2 rps2-rpoC2 GAGCCCTTATTGCAGCTGAT TTATCGATCCCAGGGGGTAC 983–988 1.000 80.9
rps2-rpoC2_p3 rps2-rpoC2 AACATAATGACACCGAGCCC GAAGGTTGGAACGAGCGTAT 1113–1118 1.000 80.8
rps2-rpoC2_p4 rps2-rpoC2 GACATACCACCGAGCCATTT GAAGGTTGGAACGAGCGTAT 1139–1144 1.000 80.8
rps2-rpoC2_p5 rps2-rpoC2 GCGAGATCTGGGTCACAATT GAAGGTTGGAACGAGCGTAT 1424–1429 1.000 80.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCGGGTATTGTGGACATTCC TAAAGGATTTGCAGTCCCCC 1294–1312 1.000 75.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGGGTATTGTGGACATTCCC TAAAGGATTTGCAGTCCCCC 1293–1311 1.000 75.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA TAAAGGATTTGCAGTCCCCC 1277–1295 1.000 75.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCCCTCATTTCCATTCCGG TAAAGGATTTGCAGTCCCCC 1278–1296 1.000 75.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCAAGCCCTGATCAATGAA TAAAGGATTTGCAGTCCCCC 1348–1366 1.000 74.2
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 1113–1116 1.000 69.7
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 1062–1065 1.000 68.8
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 1061–1064 1.000 68.8
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTGTTCATTCT 1060–1063 1.000 68.4
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 1119–1122 1.000 68.2
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTGGCTGAGTGGTTGATAG 235–240 1.000 82.5
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 224–229 1.000 82.5
psbC-trnS-UGA_p3 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GCTGAGTGGTTGATAGCTCC 231–236 1.000 82.4
psbC-trnS-UGA_p4 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGCTGAGTGGTTGATAGCTC 232–237 1.000 82.4
psbC-trnS-UGA_p5 psbC-trnS-UGA TTCCATGACCCCTCTTAGCT GGTGGCTGAGTGGTTGATAG 227–232 1.000 81.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Galanthus elwesii PP853202.1 158019 View on NCBI ↗
Galanthus nivalis OR884993.1 157538 View on NCBI ↗
Galanthus reginae-olgae PP853203.1 157759 View on NCBI ↗
Galanthus woronowii PP853204.1 156203 View on NCBI ↗