Markers + reference

Astragalus

66 species · Fabaceae · Fabales

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Species 66
Genome length 118–126 kb
Candidate markers 227
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 227 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnL-UAA-trnT-UGU Genome 1044 0.0645 0.97 81.7 yes View details
accD Genome 1503 0.0856 0.88 75.6 yes View details
trnN-GUU-ycf1 Genome 616 0.1158 0.79 72.9 yes View details
ycf1 Genome 5196 0.0712 0.99 76.1 yes View details
trnC-GCA-rpoB Genome 1151 0.0531 0.99 87.7 yes View details
trnP-UGG-psaJ Genome 558 0.0596 0.99 85.9 yes View details
psbE-petL Genome 1132 0.0599 1.00 85.4 yes View details
trnR-ACG-trnN-GUU Genome 487 0.0811 0.99 84.9 yes View details
psbD-trnT-GGU Genome 1066 0.0506 0.99 84.6 yes View details
matK-trnK-UUU Genome 715 0.0339 1.00 83.5 yes View details
petN-trnC-GCA Genome 956 0.0535 0.99 83.3 yes View details
petA-psbJ Genome 886 0.0499 0.98 82.3 yes View details
rpl32-ndhF Genome 744 0.0590 0.99 81.6 yes View details
trnG-UCC-trnS-GCU Genome 648 0.0612 0.96 80.9 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
matK-trnK-UUU_p1 matK-trnK-UUU AGTCCTGTTGGCGAGATCTA TCGATTCGCCTTCACGATTT 853–894 0.909 86.5
matK-trnK-UUU_p2 matK-trnK-UUU GAAGTCCTGTTGGCGAGATC TCGATTCGCCTTCACGATTT 855–896 0.924 85.5
matK-trnK-UUU_p3 matK-trnK-UUU AGTCCTGTTGGCGAGATCTA ATCGATTCGCCTTCACGATT 854–895 0.894 84.1
matK-trnK-UUU_p4 matK-trnK-UUU GAAGTCCTGTTGGCGAGATC ATCGATTCGCCTTCACGATT 856–897 0.909 83.1
matK-trnK-UUU_p5 matK-trnK-UUU AGTCCTGTTGGCGAGATCTA AATCGATTCGCCTTCACGAT 855–896 0.879 82.7
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU TGAGCTATCCCGACCATTCT CGAAGCCATACCCAATCGAA 2082–2527 0.970 89.7
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TGAGCTATCCCGACCATTCT TTGACCCTTTCGCTTTTCCA 2011–2456 0.970 89.6
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU TGAGCTATCCCGACCATTCT AGGTCCTCTGTAACGTGACA 1797–2242 0.924 88.2
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU GCTTCCATTGAGTCTCTGCA AGGTCCTCTGTAACGTGACA 1320–1709 0.924 88.1
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU CTCAGGATTGCCCATTGTGA AGGTCCTCTGTAACGTGACA 1265–1620 0.894 86.6
psbD-trnT-GGU_p1 psbD-trnT-GGU CACAAAAACGAAACGGTCCC GGCGTAAGTCATCGGTTCAA 827–1227 0.970 87.2
psbD-trnT-GGU_p2 psbD-trnT-GGU CCACAAAAACGAAACGGTCC GGCGTAAGTCATCGGTTCAA 828–1228 0.970 87.2
psbD-trnT-GGU_p3 psbD-trnT-GGU CCCACAAAAACGAAACGGTC GGCGTAAGTCATCGGTTCAA 829–1229 0.970 87.2
psbD-trnT-GGU_p4 psbD-trnT-GGU ACAAAAACGAAACGGTCCCT GGCGTAAGTCATCGGTTCAA 826–1226 0.970 86.6
psbD-trnT-GGU_p5 psbD-trnT-GGU AACCCACAAAAACGAAACGG GGCGTAAGTCATCGGTTCAA 831–1231 0.970 86.3
petN-trnC-GCA_p1 petN-trnC-GCA TTAAAGCAGCCCAAGCAAGA CGATATGGCCGAGTGGTAAG 681–1082 0.970 90.2
petN-trnC-GCA_p2 petN-trnC-GCA CAGCCCAAGCAAGACTTACT CGATATGGCCGAGTGGTAAG 675–1076 0.970 88.7
petN-trnC-GCA_p3 petN-trnC-GCA TTAAAGCAGCCCAAGCAAGA TTTCCCCAGTTCAAATCCGG 80–1042 0.909 87.7
petN-trnC-GCA_p4 petN-trnC-GCA CAGCCCAAGCAAGACTTACT TTTCCCCAGTTCAAATCCGG 80–1036 0.909 86.2
petN-trnC-GCA_p5 petN-trnC-GCA TTAAAGCAGCCCAAGCAAGA GGGGGACTGCAAATCCTTTT 687–1060 0.909 85.5
trnC-GCA-rpoB_p1 trnC-GCA-rpoB CTTACCACTCGGCCATATCG TTCATTTCCAACCCCAAGCA 1041–1273 0.939 88.3
trnC-GCA-rpoB_p2 trnC-GCA-rpoB CCGGATTTGAACTGGGGAAA TTCATTTCCAACCCCAAGCA 1081–1313 0.909 87.0
trnC-GCA-rpoB_p3 trnC-GCA-rpoB CTTACCACTCGGCCATATCG TCATTTCCAACCCCAAGCAT 1040–1272 0.939 86.5
trnC-GCA-rpoB_p4 trnC-GCA-rpoB ATTCTCTTGTCGATCAGGCG TTCATTTCCAACCCCAAGCA 1105–1337 0.894 85.3
trnC-GCA-rpoB_p5 trnC-GCA-rpoB CCGGATTTGAACTGGGGAAA TCATTTCCAACCCCAAGCAT 1080–1312 0.909 85.1
trnG-UCC-trnS-GCU_p1 trnG-UCC-trnS-GCU GTCCTTAGAACGAATCGCACT CAATCCGACGCTTTAGTCCA 520–865 0.970 81.8
trnG-UCC-trnS-GCU_p2 trnG-UCC-trnS-GCU GTCCTTAGAACGAATCGCACT AATCCGACGCTTTAGTCCAC 519–864 0.970 81.8
trnG-UCC-trnS-GCU_p3 trnG-UCC-trnS-GCU ACGAATCGCACTTTTACCACT CAATCCGACGCTTTAGTCCA 511–856 0.970 80.9
trnG-UCC-trnS-GCU_p4 trnG-UCC-trnS-GCU ACGAATCGCACTTTTACCACT AATCCGACGCTTTAGTCCAC 510–855 0.970 80.8
trnG-UCC-trnS-GCU_p5 trnG-UCC-trnS-GCU ACGAATCGCACTTTTACCAC CAATCCGACGCTTTAGTCCA 511–856 0.970 80.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (66)

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

Species Accession Length (bp) Link
Astragalus acutirostris NC_063479.1 123082 View on NCBI ↗
Astragalus adsurgens NC_085710.1 122796 View on NCBI ↗
Astragalus agnicidus NC_063478.1 123777 View on NCBI ↗
Astragalus agrestis NC_077551.1 123052 View on NCBI ↗
Astragalus alpinus PP328800.1 122967 View on NCBI ↗
Astragalus americanus NC_063480.1 122398 View on NCBI ↗
Astragalus ampullarioides NC_063481.1 122944 View on NCBI ↗
Astragalus ampullarius NC_063482.1 122592 View on NCBI ↗
Astragalus arbuscula NC_077550.1 123613 View on NCBI ↗
Astragalus arpilobus NC_077549.1 123054 View on NCBI ↗
Astragalus arrectus NC_063483.1 122721 View on NCBI ↗
Astragalus australis PP328801.1 123943 View on NCBI ↗
Astragalus bhotanensis NC_047381.1 123278 View on NCBI ↗
Astragalus bicristatus NC_063484.1 122963 View on NCBI ↗
Astragalus bolanderi NC_063485.1 122022 View on NCBI ↗
Astragalus canadensis var. brevidens NC_060799.1 123013 View on NCBI ↗
Astragalus chinensis PV870770.1 122346 View on NCBI ↗
Astragalus clevelandii NC_063486.1 122656 View on NCBI ↗
Astragalus cognatus NC_077548.1 123215 View on NCBI ↗
Astragalus degensis PX999255.1 122187 View on NCBI ↗
Astragalus dilutus NC_077547.1 123395 View on NCBI ↗
Astragalus effusus PV870843.1 124284 View on NCBI ↗
Astragalus ellipsoideus PZ307143.1 123333 View on NCBI ↗
Astragalus floridus OR491695.1 122441 View on NCBI ↗
Astragalus galactites NC_058825.1 126117 View on NCBI ↗
Astragalus gummifer NC_047251.1 123425 View on NCBI ↗
Astragalus gypsodes NC_063487.1 122194 View on NCBI ↗
Astragalus iranicus LC764834.1 121050 View on NCBI ↗
Astragalus jiuquanensis NC_077545.1 118399 View on NCBI ↗
Astragalus khasianus PX999253.1 124682 View on NCBI ↗
Astragalus laxmannii NC_052923.1 122844 View on NCBI ↗
Astragalus leucocephalus NC_085734.1 123412 View on NCBI ↗
Astragalus lhorongensis PZ117412.1 122884 View on NCBI ↗
Astragalus lithophilus NC_077544.1 123196 View on NCBI ↗
Astragalus lonchocarpus PV870772.1 123548 View on NCBI ↗
Astragalus melilotoides var. tenuis OP723862.1 123012 View on NCBI ↗
Astragalus membranaceus NC_084335.1 123791 View on NCBI ↗
Astragalus mesoleios LC764836.1 122171 View on NCBI ↗
Astragalus mongholicus NC_029828.1 123582 View on NCBI ↗
Astragalus mongholicus var. dahuricus MW719856.1 122789 View on NCBI ↗
Astragalus mongholicus var. nakaianus NC_028171.1 123633 View on NCBI ↗
Astragalus muliensis OR491696.1 122836 View on NCBI ↗
Astragalus nuratensis PX928918.1 122316 View on NCBI ↗
Astragalus nuttallianus var. imperfectus MZ923750.1 122840 View on NCBI ↗
Astragalus obscurus NC_063489.1 121590 View on NCBI ↗
Astragalus odoratus LC764837.1 123622 View on NCBI ↗
Astragalus oxyglottis NC_077543.1 123067 View on NCBI ↗
Astragalus pallasii NC_077542.1 119046 View on NCBI ↗
Astragalus pattersonii NC_063490.1 122969 View on NCBI ↗
Astragalus pectinatus NC_063491.1 123069 View on NCBI ↗
Astragalus polycladus PV910878.1 122868 View on NCBI ↗
Astragalus psilosepalus OR491697.1 123560 View on NCBI ↗
Astragalus purpurinus PP937056.1 123912 View on NCBI ↗
Astragalus rumpens PX711949.1 123551 View on NCBI ↗
Astragalus scabrisetus NC_077541.1 123658 View on NCBI ↗
Astragalus serenoi var. serenoi MZ923754.1 123386 View on NCBI ↗
Astragalus sieversianus NC_077540.1 121740 View on NCBI ↗
Astragalus stipulatus OR491698.1 123448 View on NCBI ↗
Astragalus strictus PX999251.1 122847 View on NCBI ↗
Astragalus tephrodes var. chloridae MZ923755.1 122693 View on NCBI ↗
Astragalus toanus var. toanus MZ923756.1 122573 View on NCBI ↗
Astragalus tumbatsica OR491699.1 124662 View on NCBI ↗
Astragalus vulpinus NC_077539.1 122222 View on NCBI ↗
Astragalus wootonii var. wootonii MZ923757.1 122915 View on NCBI ↗
Astragalus yunnanensis subsp. incanus PV156653.1 125549 View on NCBI ↗
Astragalus zerabulaki PX711948.1 123542 View on NCBI ↗