Markers + reference

Melilotus

2 species · Fabaceae · Fabales

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Species 2
Genome length 127–127 kb
Candidate markers 221
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 221 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
clpP Genome 3108 0.2888 0.88 78.8 yes View details
trnL-CAA-ycf2 Genome 509 0.4919 0.85 79.0 yes View details
ycf2 Genome 5619 0.4784 0.79 72.9 yes View details
trnI-CAU-ndhB Genome 1092 0.3429 0.93 83.0 yes View details
rps18 Genome 378 0.0596 0.98 80.5 yes View details
ycf1-rps15 Genome 512 0.0804 0.95 80.1 yes View details
rpl23-trnL-CAA Genome 318 0.1902 0.96 76.8 yes View details
rrn4.5-rrn5 Genome 230 0.0870 1.00 76.0 yes View details
trnN-GUU-ycf1 Genome 545 0.0704 0.86 75.2 yes View details
petB-petD Genome 195 0.0703 0.95 75.0 yes View details
trnL-CAA Genome 81 0.6429 0.86 74.9 yes View details
ycf2-trnI-CAU Genome 116 0.5439 0.98 74.2 yes View details
trnI-CAU Genome 74 0.5479 0.99 73.8 yes View details
clpP-psbB Genome 377 0.0567 0.94 73.6 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
rps18_p1 rps18 TCTTACAACGCAACAACCTCA AGAAATGGGATTTTCGGTATAGGA 528–530 1.000 44.7
rps18_p2 rps18 TCTTACAACGCAACAACCTCA TGGGATTTTCGGTATAGGAA 523–525 1.000 44.7
rps18_p3 rps18 CTTACAACGCAACAACCTCA AGAAATGGGATTTTCGGTATAGGA 527–529 1.000 44.7
rps18_p4 rps18 TCTTACAACGCAACAACCTCA ATGGGATTTTCGGTATAGGA 524–526 1.000 44.7
rps18_p5 rps18 TCTTACAACGCAACAACCTCA GAAATGGGATTTTCGGTATAGGA 527–529 1.000 44.7
clpP_p1 clpP AGCATATGTTACAAGGGCCG AGGATTAGCCGCTTCAATGG 2004 0.500 59.5
clpP_p2 clpP CCTGCTGGAGATGGACAATC AGGATTAGCCGCTTCAATGG 1807 0.500 59.5
clpP_p3 clpP ATCAACAATTCCGTGGGCTT AGGATTAGCCGCTTCAATGG 2797 0.500 59.2
clpP_p4 clpP CTTGTCCTTGTGCTTGTCCT AGCACAAGGACAAGCACAAT 328 0.500 57.4
clpP_p5 clpP AGCATATGTTACAAGGGCCG AGCACAAGGACAAGCACAAT 805 0.500 57.3
clpP-psbB_p1 clpP-psbB CCATTGAAGCGGCTAATCCT AACAGGGTCAGAGGGATCAA 852–867 1.000 86.1
clpP-psbB_p2 clpP-psbB CCATTGAAGCGGCTAATCCT ACAGGGTCAGAGGGATCAAA 851–866 1.000 86.1
clpP-psbB_p3 clpP-psbB CCATTGAAGCGGCTAATCCT AAAAGCACAAGCCCGAAAAC 1024–1039 1.000 84.9
clpP-psbB_p4 clpP-psbB CCATTGAAGCGGCTAATCCT AATGCGCCAAAACCAAAACA 1166–1181 1.000 84.5
clpP-psbB_p5 clpP-psbB CCATTGAAGCGGCTAATCCT GCTTGTACCCTTCCGGTTAG 1238–1253 1.000 84.3
petB-petD_p1 petB-petD TAAGCAAGGCATTTCCGGTC GTTCAAGTCACACACTCCCA 243–244 1.000 80.6
petB-petD_p2 petB-petD CAAGGCATTTCCGGTCCTTT GTTCAAGTCACACACTCCCA 239–240 1.000 79.1
petB-petD_p3 petB-petD GTAAGCAAGGCATTTCCGGT GTTCAAGTCACACACTCCCA 244–245 1.000 78.3
petB-petD_p4 petB-petD TAAGCAAGGCATTTCCGGTC AGTTCAAGTCACACACTCCC 244–245 1.000 78.2
petB-petD_p5 petB-petD AAGGCATTTCCGGTCCTTTA GTTCAAGTCACACACTCCCA 238–239 1.000 78.0
rpl23-trnL-CAA_p1 rpl23-trnL-CAA AAACCGCACTCAAAGGTAGG GTCTCGCGTGTCTACCATTT 1052 0.500 59.1
rpl23-trnL-CAA_p2 rpl23-trnL-CAA AAACCGCACTCAAAGGTAGG CTCGCGTGTCTACCATTTCA 1050 0.500 59.1
rpl23-trnL-CAA_p3 rpl23-trnL-CAA AAACCGCACTCAAAGGTAGG GTGATCTGCTGGCGAACTTA 1150 0.500 59.1
rpl23-trnL-CAA_p4 rpl23-trnL-CAA CCCTGCGGTAATGATTCCTC GTCTCGCGTGTCTACCATTT 802 0.500 59.0
rpl23-trnL-CAA_p5 rpl23-trnL-CAA CCCTGCGGTAATGATTCCTC CTCGCGTGTCTACCATTTCA 800 0.500 59.0
trnL-CAA_p1 trnL-CAA CTCGGGATGACATGACGATC GTGATCTGCTGGCGAACTTA 243 0.500 59.5
trnL-CAA_p2 trnL-CAA CTCGGGATGACATGACGATC TCTGCTGGCGAACTTATTCC 239 0.500 59.3
trnL-CAA_p3 trnL-CAA CTCGGGATGACATGACGATC CTGCTGGCGAACTTATTCCT 238 0.500 59.3
trnL-CAA_p4 trnL-CAA CTCGGGATGACATGACGATC ACGGGGTGAGATTTGTCCTA 545 0.500 59.1
trnL-CAA_p5 trnL-CAA CTCGGGATGACATGACGATC CTTTCTCGTCGTCTCATGGG 666 0.500 58.9

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
Melilotus albus NC_041419.1 127205 View on NCBI ↗
Melilotus officinalis NC_070051.1 126946 View on NCBI ↗