Markers + reference

Maianthemum

9 species · Asparagaceae · Asparagales

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Species 9
Genome length 157–158 kb
Candidate markers 272
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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1281 0.0185 1.00 70.4 yes View details
trnS-GCU-trnG-UCC LSC 1288 0.0179 0.99 65.1 yes View details
rpoB-trnC-GCA LSC 1260 0.0121 1.00 58.7 yes View details
trnC-GCA-petN LSC 924 0.0143 1.00 60.4 yes View details
ndhC-trnV-UAC LSC 1664 0.0106 1.00 54.8 yes View details
petA-psbJ LSC 1072 0.0140 1.00 57.1 yes View details
psbE-petL LSC 1319 0.0137 1.00 70.1 yes View details
psaJ-rpl33 LSC 582 0.0233 0.95 72.8 yes View details
ndhF-rpl32 SSC 988 0.0183 0.98 67.2 yes View details
rpl32-trnL-UAG SSC 955 0.0289 0.99 72.1 yes View details
psbI-trnS-GCU LSC 123 0.0379 0.98 72.8 yes View details
psaC-ndhE SSC 374 0.0199 1.00 72.1 yes View details
trnT-UGU-trnL-UAA LSC 940 0.0120 0.99 70.3 yes View details
rps19-psbA LSC 122 0.0200 1.00 69.1 no View details
atpF-atpH LSC 493 0.0117 1.00 67.9 yes View details
rps3-rpl22 LSC 56 0.0625 0.89 65.8 yes View details
psbM-trnD-GUC LSC 730 0.0090 1.00 63.4 yes View details
rbcL-accD LSC 696 0.0128 0.98 62.0 yes View details
trnH-GUG-rpl2 IRb 43 0.0297 1.00 61.7 yes View details
rpl2-trnH-GUG IRa 43 0.0297 1.00 61.7 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 95 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 520–1379 1.000 88.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 520–1383 1.000 83.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 520–1409 1.000 83.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 512–1371 1.000 83.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 519–1378 1.000 82.6
psbI-trnS-GCU_p1 psbI-trnS-GCU CTTATCTAACGATCCGGGCC ATTGGGAGAGATGGCTGAGT 254–2225 1.000 78.9
psbI-trnS-GCU_p2 psbI-trnS-GCU CTTATCTAACGATCCGGGCC GGGTTCGAATCCCTCTCTCT 185–2156 1.000 78.5
psbI-trnS-GCU_p3 psbI-trnS-GCU CTTATCTAACGATCCGGGCC GTGGACTAAAGCGGCAGATT 236–2207 1.000 77.8
psbI-trnS-GCU_p4 psbI-trnS-GCU CTTATCTAACGATCCGGGCC TGGACTAAAGCGGCAGATTG 235–2206 1.000 77.8
psbI-trnS-GCU_p5 psbI-trnS-GCU CTTATCTAACGATCCGGGCC TTCGAATCCCTCTCTCTCCG 182–2153 1.000 77.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATCAGAGGGAACGGAGAGAG TACCACTAAACTATACCCGC 1282–1464 1.000 55.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATCAGAGGGAACGGAGAGAG TTACCACTAAACTATACCCGC 1283–1465 1.000 53.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GGAACGGAGAGAGAGGGATT TACCACTAAACTATACCCGC 1275–1457 1.000 53.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC TACCACTAAACTATACCCGC 1217–1399 1.000 53.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCTGCCGCTTTAGTCCA TACCACTAAACTATACCCGC 1218–1400 1.000 53.6
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG ATTTATGGACTGGTCGTGGC 80–625 1.000 85.5
atpF-atpH_p2 atpF-atpH CAGTGGCCTAAGGAAACGAA ATTTATGGACTGGTCGTGGC 311–597 1.000 84.8
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TCGTGGCATTAGCGCTTTTA 326–612 1.000 83.4
atpF-atpH_p4 atpF-atpH CAGTGGCCTAAGGAAACGAA TCGTGGCATTAGCGCTTTTA 298–584 1.000 83.0
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CGTGGCATTAGCGCTTTTAT 325–611 1.000 79.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGAGGTTCCCAGGGAATTCA AGAATCAGGAGAACCCACCA 2189–2209 1.000 83.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GAAAATACCGGATCCCCACC AGAATCAGGAGAACCCACCA 2569–2589 1.000 83.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GAAAATACCGGATCCCCACC AATCGAGTATTGACACGCCC 2153–2171 1.000 82.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GAAAATACCGGATCCCCACC ATTGACACGCCCACTTAGTC 2145–2163 1.000 82.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GAAAATACCGGATCCCCACC GAGTATTGACACGCCCACTT 2149–2159 0.889 77.3
trnC-GCA-petN_p1 trnC-GCA-petN GGGGGACTGCAAATCCTTTA TTAAAGCAGCCCAAGCAAGA 1000–1014 1.000 79.4
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTA AGTCCACTCCTTCCCCATAC 1052–1066 1.000 78.3
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTA GTCCACTCCTTCCCCATACT 1051–1065 1.000 78.3
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTA GAGTCCACTCCTTCCCCATA 1053–1067 1.000 77.9
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTA AGCAATTAGTAGTGCCCAGC 80–1082 0.889 74.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Maianthemum bicolor NC_035970.1 157176 View on NCBI ↗
Maianthemum bifolium NC_070128.1 156961 View on NCBI ↗
Maianthemum dilatatum NC_039133.1 156921 View on NCBI ↗
Maianthemum fuscum NC_065357.1 156711 View on NCBI ↗
Maianthemum henryi NC_057254.1 157728 View on NCBI ↗
Maianthemum japonicum NC_070126.1 157163 View on NCBI ↗
Maianthemum lichiangense PV087155.1 156799 View on NCBI ↗
Maianthemum purpureum NC_080371.1 157203 View on NCBI ↗
Maianthemum racemosum PV087156.1 156842 View on NCBI ↗