Markers + reference

Medicago

21 species · Fabaceae · Fabales

Back to catalogue

Species 21
Genome length 121–127 kb
Candidate markers 227
Primer pairs 75

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 9 remaining regions by MarkerSeek score (out of 227 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnQ-UUG-accD Genome 1194 0.0794 1.00 75.9 yes View details
accD Genome 2190 0.1180 0.76 71.5 yes View details
rps12-clpP Genome 869 0.1616 0.93 76.4 yes View details
clpP Genome 1219 0.0421 0.99 76.0 yes View details
rpl23-trnI-CAU Genome 631 0.1145 0.76 76.8 yes View details
ycf2 Genome 5529 0.0338 1.00 64.9 yes View details
rrn16-trnI-GAU Genome 309 0.0687 1.00 85.2 yes View details
trnG-GCC-psbZ Genome 613 0.0568 0.90 81.2 yes View details
psbD-trnT-GGU Genome 1441 0.0199 1.00 78.8 yes View details
trnV-UAC-ndhC Genome 449 0.0327 0.98 78.0 yes View details
psbM-petN Genome 664 0.0253 1.00 78.0 yes View details
ycf1-rps15 Genome 424 0.0708 0.97 77.6 yes View details
atpA-trnR-UCU Genome 204 0.0501 1.00 76.7 yes View details
trnL-UAA-trnT-UGU Genome 1212 0.0244 0.98 75.6 yes View details
trnH-GUG-psbA Genome 413 0.0317 0.99 75.2 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 313–512 0.905 86.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 327–526 0.905 86.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 326–525 0.905 86.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 328–527 0.905 86.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GCGAATGACGGGAATTGAAC TTCCCTCTAGACCTAGCTGC 365–564 0.905 86.2
trnV-UAC-ndhC_p1 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT GGCCCTTTTCTAATTGGAGC 416–621 1.000 80.4
trnV-UAC-ndhC_p2 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT GGCCCTTTTCTAATTGGAGCT 416–621 1.000 80.3
trnV-UAC-ndhC_p3 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT TGGCCCTTTTCTAATTGGAGC 417–622 1.000 78.1
trnV-UAC-ndhC_p4 trnV-UAC-ndhC GAAGGTCTACGGTTCGAGTC GGCCCTTTTCTAATTGGAGC 415–620 1.000 77.6
trnV-UAC-ndhC_p5 trnV-UAC-ndhC GAAGGTCTACGGTTCGAGTC GGCCCTTTTCTAATTGGAGCT 415–620 1.000 77.6
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 821–1369 1.000 90.9
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 829–1377 1.000 90.4
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GGAATCGAACCGATGACCAT 853–1401 1.000 90.0
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 861–1409 1.000 89.5
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 835–1383 1.000 89.0
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGGATAGTGGGAATCGAACC TTGCTTCTCCTGATGGTTGG 623–883 1.000 89.2
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGGATAGTGGGAATCGAACC GCTTCTCCTGATGGTTGGTC 621–881 1.000 88.7
trnG-GCC-psbZ_p3 trnG-GCC-psbZ GCGGATAGTGGGAATCGAAC TTGCTTCTCCTGATGGTTGG 624–884 1.000 86.4
trnG-GCC-psbZ_p4 trnG-GCC-psbZ GGATAGTGGGAATCGAACCC TTGCTTCTCCTGATGGTTGG 622–882 1.000 86.0
trnG-GCC-psbZ_p5 trnG-GCC-psbZ GCGGATAGTGGGAATCGAAC GCTTCTCCTGATGGTTGGTC 622–882 1.000 85.9
psbD-trnT-GGU_p1 psbD-trnT-GGU GAGCAATAGACCGGACCAAC GTGGTAGAGTAACGCCATGG 1153–1640 1.000 88.4
psbD-trnT-GGU_p2 psbD-trnT-GGU GAGCAATAGACCGGACCAAC TCAGTGGTAGAGTAACGCCA 1156–1643 1.000 88.2
psbD-trnT-GGU_p3 psbD-trnT-GGU GAGCAATAGACCGGACCAAC GGAGCCCCTTTAACTCAGTG 1170–1657 1.000 88.0
psbD-trnT-GGU_p4 psbD-trnT-GGU GAGCAATAGACCGGACCAAC GAGCCCCTTTAACTCAGTGG 1169–1656 1.000 87.9
psbD-trnT-GGU_p5 psbD-trnT-GGU AGAGCAATAGACCGGACCAA GTGGTAGAGTAACGCCATGG 1154–1641 1.000 87.7
psbM-petN_p1 psbM-petN AGCTACTGCACTCTTCATTCT AGTAAGTCTTGCTTGGGCTG 633–1077 1.000 71.9
psbM-petN_p2 psbM-petN TCGCATTTATAGCTACTGCACT AGTAAGTCTTGCTTGGGCTG 643–1087 1.000 71.3
psbM-petN_p3 psbM-petN AGCTACTGCACTCTTCATTCT ATGGGGAAGAAGTGGACTCT 573–1017 1.000 71.0
psbM-petN_p4 psbM-petN AGCTACTGCACTCTTCATTCT TCTTGCTTGGGCTGGTTTAA 627–1071 1.000 70.5
psbM-petN_p5 psbM-petN AGCTACTGCACTCTTCATTCT GTCTTGCTTGGGCTGGTTTA 628–1072 1.000 70.4

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
Medicago arborea NC_042856.1 124273 View on NCBI ↗
Medicago ciliaris NC_068652.1 124777 View on NCBI ↗
Medicago cretacea NC_042842.1 126021 View on NCBI ↗
Medicago edgeworthii NC_052706.1 122442 View on NCBI ↗
Medicago hybrida NC_027153.1 125208 View on NCBI ↗
Medicago intertexta NC_042851.1 125621 View on NCBI ↗
Medicago marina NC_042845.1 124182 View on NCBI ↗
Medicago medicaginoides PV870671.1 121129 View on NCBI ↗
Medicago monspeliaca NC_042855.1 121313 View on NCBI ↗
Medicago orbicularis NC_042850.1 125015 View on NCBI ↗
Medicago papillosa NC_027154.1 125203 View on NCBI ↗
Medicago pironae NC_042846.1 123712 View on NCBI ↗
Medicago polymorpha NC_042848.1 124066 View on NCBI ↗
Medicago praecox NC_057657.1 122724 View on NCBI ↗
Medicago radiata NC_042854.1 124564 View on NCBI ↗
Medicago sativa PP328804.1 125507 View on NCBI ↗
Medicago sativa subsp. caerulea OM009291.1 121383 View on NCBI ↗
Medicago sativa subsp. glomerata MK460494.1 125889 View on NCBI ↗
Medicago sativa subsp. sativa NC_042841.1 125330 View on NCBI ↗
Medicago tetraprostrata NC_042844.1 126778 View on NCBI ↗
Medicago x varia NC_068269.1 125698 View on NCBI ↗