Markers + reference

Lotus

13 species · Fabaceae · Fabales

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Species 13
Genome length 150–152 kb
Candidate markers 265
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhJ-trnF-GAA LSC 601 0.0367 1.00 80.1 yes View details
trnL-UAA-trnT-UGU LSC 962 0.0526 0.90 85.4 yes View details
trnE-UUC-trnY-GUA LSC 286 0.1269 0.21 60.6 yes View details
petN-trnC-GCA LSC 1141 0.0315 0.97 81.1 yes View details
atpA-trnR-UCU LSC 295 0.0326 0.99 65.9 yes View details
trnR-UCU-trnG-UCC LSC 205 0.0821 0.90 71.7 yes View details
trnG-UCC-trnS-GCU LSC 786 0.0350 0.96 79.5 yes View details
trnQ-UUG-rps16 LSC 497 0.0428 0.89 78.5 yes View details
rps16-accD LSC 540 0.0386 0.99 76.7 yes View details
trnP-UGG-psaJ LSC 699 0.0371 0.94 75.1 yes View details
rps11-rpl36 LSC 345 0.0460 0.98 75.6 yes View details
ndhF-rpl32 SSC 783 0.0334 0.99 77.2 yes View details
petA-psbJ LSC 804 0.0242 0.99 75.3 yes View details
psbA-trnK-UUU LSC 292 0.0404 0.96 74.5 yes View details
trnW-CCA-trnP-UGG LSC 179 0.0473 1.00 74.1 yes View details
trnH-GUG-psbA LSC 278 0.0552 0.98 73.9 yes View details
atpH-atpF LSC 542 0.0314 0.97 73.0 yes View details
rpl36-rps8 LSC 358 0.0349 0.99 72.8 yes View details
rps4-trnS-GGA LSC 228 0.0297 0.98 72.4 yes View details
trnC-GCA-rpoB LSC 914 0.0306 0.97 71.9 yes View details
rpl20-rps12 LSC 844 0.0207 0.98 71.8 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTGACGGTATGCCTCTAGGA 866–914 1.000 84.9
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CTGACGGTATGCCTCTAGGA 852–900 0.923 81.7
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCTGACGGTATGCCTCTAGG 853–901 0.923 81.7
trnH-GUG-psbA_p4 trnH-GUG-psbA TTTTTGGTATGGGCGAACGA CTGACGGTATGCCTCTAGGA 921–930 0.308 54.5
trnH-GUG-psbA_p5 trnH-GUG-psbA TTTTTGGTATGGGCGAACGA TCTGACGGTATGCCTCTAGG 922–931 0.308 54.5
psbA-trnK-UUU_p1 psbA-trnK-UUU CCCCATAGGTTTTCGCTCTC CGACTAGTTCCGGGTTCAAG 319–394 1.000 89.8
psbA-trnK-UUU_p2 psbA-trnK-UUU CCCCATAGGTTTTCGCTCTC CTAGTTCCGGGTTCAAGTCC 316–391 1.000 86.8
psbA-trnK-UUU_p3 psbA-trnK-UUU CCCATAGGTTTTCGCTCTCG CGACTAGTTCCGGGTTCAAG 318–393 1.000 86.7
psbA-trnK-UUU_p4 psbA-trnK-UUU GCTCTCGCGTCTCTCTAAAA CGACTAGTTCCGGGTTCAAG 305–380 1.000 86.0
psbA-trnK-UUU_p5 psbA-trnK-UUU TACAGAAGCGACCCCATAGG CGACTAGTTCCGGGTTCAAG 330–405 1.000 85.2
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA AATGCCCGAAAGCTGGATAG CCTCGTGTCACCAGTTCAAA 708–776 1.000 91.3
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA TTTAATGCCCGAAAGCTGGA CCTCGTGTCACCAGTTCAAA 711–779 1.000 89.8
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA AATGCCCGAAAGCTGGATAG AATCCTCGTGTCACCAGTTC 711–779 1.000 88.0
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA TTAATGCCCGAAAGCTGGAT CCTCGTGTCACCAGTTCAAA 710–778 1.000 88.0
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA TTTAATGCCCGAAAGCTGGA AATCCTCGTGTCACCAGTTC 714–782 1.000 86.6
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 934–1023 1.000 90.9
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 942–1031 1.000 90.4
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GGAATCGAACCGATGACCAT 966–1055 1.000 90.0
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 974–1063 1.000 89.5
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU CCCATTGTGAATTCCAGGGT GCGATGCTCTAACCTCTGAG 1027–1116 1.000 89.0
rps4-trnS-GGA_p1 rps4-trnS-GGA TGACTCTTCAGCCATTCCAA AGGCTTTTTGCTTACCGAGG 377–391 1.000 75.2
rps4-trnS-GGA_p2 rps4-trnS-GGA TTGACTCTTCAGCCATTCCA AGGCTTTTTGCTTACCGAGG 378–392 1.000 75.2
rps4-trnS-GGA_p3 rps4-trnS-GGA TGACTCTTCAGCCATTCCAA TTTTGCTTACCGAGGGTTCG 372–386 1.000 75.2
rps4-trnS-GGA_p4 rps4-trnS-GGA TTGACTCTTCAGCCATTCCA TTTTGCTTACCGAGGGTTCG 373–387 1.000 75.1
rps4-trnS-GGA_p5 rps4-trnS-GGA TTGACTCTTCAGCCATTCCAA AGGCTTTTTGCTTACCGAGG 378–392 1.000 73.2
trnE-UUC-trnY-GUA_p1 trnE-UUC-trnY-GUA AAGTATGCCCCCATCGTCTA CCAGCGTAGACATATTGCCA 203–429 1.000 89.3
trnE-UUC-trnY-GUA_p2 trnE-UUC-trnY-GUA AAGTATGCCCCCATCGTCTA ACCAGCGTAGACATATTGCC 204–430 1.000 89.3
trnE-UUC-trnY-GUA_p3 trnE-UUC-trnY-GUA TCTCTTTCAAGGAGGCAACG CCAGCGTAGACATATTGCCA 168–394 1.000 88.7
trnE-UUC-trnY-GUA_p4 trnE-UUC-trnY-GUA TCTCTTTCAAGGAGGCAACG ACCAGCGTAGACATATTGCC 169–395 1.000 88.7
trnE-UUC-trnY-GUA_p5 trnE-UUC-trnY-GUA AAGTATGCCCCCATCGTCTA CGAATTTACAGTCCGTCCCC 182–408 1.000 88.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Lotus conjugatus PQ539372.1 151097 View on NCBI ↗
Lotus corniculatus PV870832.1 150805 View on NCBI ↗
Lotus corniculatus subsp. corniculatus PP203130.1 150804 View on NCBI ↗
Lotus dorycnium PQ539369.1 150685 View on NCBI ↗
Lotus fulgurans PV870842.1 151135 View on NCBI ↗
Lotus graecus PQ539373.1 151118 View on NCBI ↗
Lotus herbaceus PQ539374.1 151071 View on NCBI ↗
Lotus hirsutus PQ539375.1 151144 View on NCBI ↗
Lotus japonicus NC_002694.1 150519 View on NCBI ↗
Lotus maritimus PP203131.1 151044 View on NCBI ↗
Lotus ornithopodioides PQ539376.1 151201 View on NCBI ↗
Lotus palustris PQ539377.1 151524 View on NCBI ↗
Lotus tetragonolobus PQ539378.1 150069 View on NCBI ↗