Markers + reference

Phlegmariurus

2 species · Lycopodiaceae · Lycopodiales

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Species 2
Genome length 150–150 kb
Candidate markers 245
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 245 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl32-trnL-UAG Genome 1041 0.4386 0.86 81.1 yes View details
ndhD Genome 1473 0.4523 0.95 83.3 yes View details
ndhA Genome 1931 0.4997 0.83 79.3 yes View details
ndhH Genome 1182 0.5005 0.86 81.1 yes View details
rps15-ycf1 Genome 539 0.4425 0.97 80.5 yes View details
ycf1 Genome 4710 0.4647 0.81 73.9 yes View details
trnG-UCC-trnR-UCU Genome 1332 0.0758 0.96 84.2 yes View details
trnA-UGC-rrn23 Genome 1016 0.0394 0.97 83.0 yes View details
psbB-clpP Genome 1054 0.0440 0.88 82.6 yes View details
ndhG Genome 561 0.4372 0.88 81.1 yes View details
ccsA Genome 1032 0.4581 0.83 80.3 yes View details
trnL-CAA-ndhB Genome 956 0.0700 0.91 79.0 yes View details
atpH-atpI Genome 829 0.0586 0.95 78.8 yes View details
rps4-trnS-GGA Genome 398 0.0678 1.00 78.2 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbB-clpP_p1 psbB-clpP AACTAACGCGGTATGCATCA TACGTCAATCCAAACGGCAT 1114–1213 1.000 83.6
psbB-clpP_p2 psbB-clpP ACTAACGCGGTATGCATCAA ATACGTCAATCCAAACGGCA 1114–1213 1.000 83.6
psbB-clpP_p3 psbB-clpP ACTAACGCGGTATGCATCAA TACGTCAATCCAAACGGCAT 1113–1212 1.000 83.6
psbB-clpP_p4 psbB-clpP TAACGCGGTATGCATCAAGT ATACGTCAATCCAAACGGCA 1112–1211 1.000 83.6
psbB-clpP_p5 psbB-clpP TAACGCGGTATGCATCAAGT TACGTCAATCCAAACGGCAT 1111–1210 1.000 83.6
rps4-trnS-GGA_p1 rps4-trnS-GGA CACTACAGAGTGTGGGATTGG CTCTTGCTTACCGAGGGTTC 539–565 1.000 75.6
rps4-trnS-GGA_p2 rps4-trnS-GGA CACTACAGAGTGTGGGATTGG GGGTTCGAATCCCTCTCTCT 525–551 1.000 74.1
rps4-trnS-GGA_p3 rps4-trnS-GGA ACTACAGAGTGTGGGATTGGT CTCTTGCTTACCGAGGGTTC 538–564 1.000 72.8
rps4-trnS-GGA_p4 rps4-trnS-GGA ACTACAGAGTGTGGGATTGG CTCTTGCTTACCGAGGGTTC 538–564 1.000 72.2
rps4-trnS-GGA_p5 rps4-trnS-GGA CTACAGAGTGTGGGATTGGT CTCTTGCTTACCGAGGGTTC 537–563 1.000 72.2
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA CTGTCCTATCCATTAGACGATGG 1404–1409 1.000 63.7
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA TGTCCTATCCATTAGACGATGG 1403–1408 1.000 63.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU TTCCAAGCTAATGATGCGGG CTGTCCTATCCATTAGACGATGG 1394–1399 1.000 61.4
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU TTCCAAGCTAATGATGCGGG TGTCCTATCCATTAGACGATGG 1393–1398 1.000 60.9
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU GCTAATGATGCGGGTTCGAT CTGTCCTATCCATTAGACGATGG 1388–1393 1.000 60.2
atpH-atpI_p1 atpH-atpI GCAGCAATAACAGAAGCAGC TTTAGCTGCTCGGAATCCAC 1442–1474 1.000 84.5
atpH-atpI_p2 atpH-atpI CGCAATACCTTCTACGGCTT TTTAGCTGCTCGGAATCCAC 1524–1556 1.000 84.4
atpH-atpI_p3 atpH-atpI TTCAGCTTCTGGTTGTCTCG TTTAGCTGCTCGGAATCCAC 1542–1574 1.000 83.7
atpH-atpI_p4 atpH-atpI TAGACCGAGTACCACACCTG TTTAGCTGCTCGGAATCCAC 2133–2145 1.000 82.9
atpH-atpI_p5 atpH-atpI CGCAATACCTTCTACGGCTT TTTTGCAACTTTAGCCGCAG 1028 0.500 58.4
trnL-CAA-ndhB_p1 trnL-CAA-ndhB CTCGCGTGTCTACCATTTCA ACCTATTTTGGTGCGGATGG 1210–1273 1.000 86.3
trnL-CAA-ndhB_p2 trnL-CAA-ndhB CTCGCGTGTCTACCATTTCA GCTTCTTGTTTTGCCTCGTG 1283–1346 1.000 86.2
trnL-CAA-ndhB_p3 trnL-CAA-ndhB CTCGCGTGTCTACCATTTCA ATTCAGTTCACGCACAGGAA 1353–1416 1.000 85.9
trnL-CAA-ndhB_p4 trnL-CAA-ndhB CTCGCGTGTCTACCATTTCA AGCTTCTTGTTTTGCCTCGT 1284–1347 1.000 85.6
trnL-CAA-ndhB_p5 trnL-CAA-ndhB CTCGCGTGTCTACCATTTCA TCTTGTTTTGCCTCGTGTCT 1280–1343 1.000 85.5
trnA-UGC-rrn23_p1 trnA-UGC-rrn23 TCCCGGCCTTCTTGGTATAA GTCTCTGGGTGCCTAGGTAT 1155–1165 1.000 82.9
trnA-UGC-rrn23_p2 trnA-UGC-rrn23 TTCCCGGCCTTCTTGGTATA GTCTCTGGGTGCCTAGGTAT 1156–1166 1.000 82.9
trnA-UGC-rrn23_p3 trnA-UGC-rrn23 TCCCGGCCTTCTTGGTATAA GAATCTCCGGATCCATGCTC 1221–1231 1.000 82.6
trnA-UGC-rrn23_p4 trnA-UGC-rrn23 TTCCCGGCCTTCTTGGTATA GAATCTCCGGATCCATGCTC 1222–1232 1.000 82.6
trnA-UGC-rrn23_p5 trnA-UGC-rrn23 TCCCGGCCTTCTTGGTATAA TCATTTTCAGCTCCCCGAAG 1203–1213 1.000 82.5

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
Phlegmariurus carinatus NC_050663.1 150349 View on NCBI ↗
Phlegmariurus phlegmaria NC_052703.1 149711 View on NCBI ↗