Markers + reference

Oxytropis

21 species · Fabaceae · Fabales

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Species 21
Genome length 122–124 kb
Candidate markers 228
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 228 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnD-GTC-psbM Genome 411 0.0676 0.96 76.3 yes View details
trnP-UGG-psaJ Genome 649 0.0499 1.00 91.5 yes View details
clpP Genome 1311 0.0579 1.00 77.7 yes View details
trnL-CAA-ndhB Genome 567 0.0533 1.00 85.4 yes View details
rps12-trnV-GAC Genome 1569 0.0450 1.00 85.0 yes View details
trnR-ACG-trnN-GUU Genome 434 0.0535 1.00 77.3 yes View details
ycf1 Genome 5085 0.0481 1.00 76.4 yes View details
ndhF Genome 2235 0.0455 1.00 75.0 yes View details
rpl23-trnI-CAU Genome 516 0.0570 0.98 92.9 yes View details
trnL-UAA-trnT-UGU Genome 1113 0.0380 1.00 88.3 yes View details
atpH-atpF Genome 643 0.0322 1.00 87.2 yes View details
ycf1-rps15 Genome 445 0.0487 1.00 86.9 yes View details
rpl2 Genome 1534 0.0428 1.00 84.6 yes View details
rpl32-ndhF Genome 729 0.0447 1.00 84.3 yes View details
ndhF-trnH-GTG Genome 242 0.0659 1.00 84.2 no View details
trnQ-UUG-accD Genome 779 0.0378 1.00 82.8 yes View details
trnL-TAG-rpl32 Genome 679 0.0472 0.99 82.8 yes View details
trnC-GCA-rpoB Genome 1049 0.0326 1.00 82.6 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 1142–1223 0.952 85.0
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GAGTCGAACCGATGACCATC 1173–1254 0.952 84.6
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1150–1231 0.952 84.4
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GAGTCGAACCGATGACCATC 1181–1262 0.952 84.1
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU CCCATTGTGAATTCCAGGGT GCGATGCTCTAACCTCTGAG 1235–1316 0.952 82.9
trnD-GTC-psbM_p1 trnD-GTC-psbM CATAGTAGAATGGCGGTCGG CCCCGGATCATCTGTCAATT 1709–1731 0.857 75.5
trnD-GTC-psbM_p2 trnD-GTC-psbM CATAGTAGAATGGCGGTCGG TCGATGAACTGGTTACGACC 1775–1797 0.810 72.5
trnD-GTC-psbM_p3 trnD-GTC-psbM AAGTATGCCCCCATCGTCTA TCGATGAACTGGTTACGACC 1753–1775 0.810 72.2
trnD-GTC-psbM_p4 trnD-GTC-psbM GAGTAATCCGTGCCGATCTC CCCCGGATCATCTGTCAATT 1221–1246 0.524 61.7
trnD-GTC-psbM_p5 trnD-GTC-psbM GAGTAATCCGTGCCGATCTC TCGATGAACTGGTTACGACC 1287–1312 0.476 58.5
trnC-GCA-rpoB_p1 trnC-GCA-rpoB CTTACCACTCGGCCATATCG TTCATTTCCAACCCCAAGCA 1088–1097 0.952 83.9
trnC-GCA-rpoB_p2 trnC-GCA-rpoB CCGGATTTGAACTGGGGAAA TTCATTTCCAACCCCAAGCA 1128–1137 0.952 83.7
trnC-GCA-rpoB_p3 trnC-GCA-rpoB CTTACCACTCGGCCATATCG TACGCCCCGATCAATGAATC 1160–1169 0.952 83.2
trnC-GCA-rpoB_p4 trnC-GCA-rpoB CCGGATTTGAACTGGGGAAA TACGCCCCGATCAATGAATC 1200–1209 0.952 83.0
trnC-GCA-rpoB_p5 trnC-GCA-rpoB CTTACCACTCGGCCATATCG AAGTTCTTCTGTTACGCCCC 1172–1181 0.905 80.3
atpH-atpF_p1 atpH-atpF CCGGAAGCAGAGGACAAAAT GATGGCCAGTAACTCAAGCA 785–839 0.952 83.9
atpH-atpF_p2 atpH-atpF TGGGCTGGTTGTAGCATTAG GATGGCCAGTAACTCAAGCA 714–768 0.952 82.4
atpH-atpF_p3 atpH-atpF CCGGAAGCAGAGGACAAAAT CGGATGGCCAGTAACTCAAG 787–841 0.952 82.1
atpH-atpF_p4 atpH-atpF CCGGAAGCAGAGGACAAAAT TGGCCAGTAACTCAAGCAAA 783–837 0.952 82.0
atpH-atpF_p5 atpH-atpF CCGGAAGCAGAGGACAAAAT ATCAAACCCGAAACTTCCGG 807–861 0.952 81.0
trnQ-UUG-accD_p1 trnQ-UUG-accD GAGGTTCGAATCCTTCCGTC TTCCGTATGTTCCTGCGATC 882–1245 0.905 82.1
trnQ-UUG-accD_p2 trnQ-UUG-accD GAGGTTCGAATCCTTCCGTC GTATGTTCCTGCGATCCACT 878–1511 0.952 81.6
trnQ-UUG-accD_p3 trnQ-UUG-accD GAGGTTCGAATCCTTCCGTC CGTATGTTCCTGCGATCCAC 879–1512 0.952 80.1
trnQ-UUG-accD_p4 trnQ-UUG-accD GAGGTTCGAATCCTTCCGTC AATTCCGTATGTTCCTGCGA 884–1247 0.905 78.3
trnQ-UUG-accD_p5 trnQ-UUG-accD TTCGGAGGTTCGAATCCTTC TTCCGTATGTTCCTGCGATC 886–1249 0.905 77.3
trnP-UGG-psaJ_p1 trnP-UGG-psaJ AAAACAAACGCGCTACCAAG TGCTAAAACCGCGAACCATA 620–769 0.952 86.0
trnP-UGG-psaJ_p2 trnP-UGG-psaJ AAAACAAACGCGCTACCAAG CGGTGCCACAGAGAGATATG 587–736 0.952 85.9
trnP-UGG-psaJ_p3 trnP-UGG-psaJ CAAAACAAACGCGCTACCAA TGCTAAAACCGCGAACCATA 621–770 0.952 85.6
trnP-UGG-psaJ_p4 trnP-UGG-psaJ TTGTACCCAAAACAAACGCG TGCTAAAACCGCGAACCATA 628–777 0.952 85.4
trnP-UGG-psaJ_p5 trnP-UGG-psaJ AAAACAAACGCGCTACCAAG ATAGAGTACTTGCCACCGGT 603–752 0.905 81.9

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
Oxytropis aciphylla NC_064361.1 122173 View on NCBI ↗
Oxytropis chiliophylla PV694277.1 122480 View on NCBI ↗
Oxytropis ciliata PV684026.1 122272 View on NCBI ↗
Oxytropis coerulea PV684031.1 122121 View on NCBI ↗
Oxytropis diversifolia NC_062618.1 122210 View on NCBI ↗
Oxytropis filiformis PV684033.1 122321 View on NCBI ↗
Oxytropis hirta PV684032.1 122356 View on NCBI ↗
Oxytropis holanshanensis PV694276.1 123621 View on NCBI ↗
Oxytropis latibracteata PV694278.1 121854 View on NCBI ↗
Oxytropis microphylla PV684029.1 122453 View on NCBI ↗
Oxytropis monophylla PV240322.1 122413 View on NCBI ↗
Oxytropis myriophylla PP836295.1 122083 View on NCBI ↗
Oxytropis neimonggolica PV684030.1 122195 View on NCBI ↗
Oxytropis ochrantha PV684024.1 122228 View on NCBI ↗
Oxytropis oxyphylla PV684036.1 122284 View on NCBI ↗
Oxytropis proboscidea PV694280.1 122363 View on NCBI ↗
Oxytropis racemosa PV684037.1 122172 View on NCBI ↗
Oxytropis sericopetala PV684035.1 122405 View on NCBI ↗
Oxytropis splendens NC_050860.1 122318 View on NCBI ↗
Oxytropis squammulosa PV684025.1 122352 View on NCBI ↗
Oxytropis xerophila PP328810.1 121763 View on NCBI ↗