Markers + reference

Phaseolus

2 species · Fabaceae · Fabales

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Species 2
Genome length 150–150 kb
Candidate markers 262
Primer pairs 80

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 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbZ-trnS-UGA LSC 366 0.0109 1.00 53.9 yes View details
psbD-trnT-GGU LSC 995 0.0363 1.00 73.0 yes View details
petN-trnC-GCA LSC 471 0.0325 0.98 66.2 yes View details
trnG-UCC-trnS-GCU LSC 620 0.0380 0.98 71.7 yes View details
accD LSC 1467 0.0469 0.96 74.4 yes View details
rps11-rpl36 LSC 327 0.0413 0.96 72.8 yes View details
rpl36-rps8 LSC 482 0.0355 0.99 63.1 yes View details
ycf1 SSC 5331 0.0208 0.99 52.3 yes View details
trnS-UGA-psbC LSC 199 0.0754 1.00 78.3 yes View details
trnG-GCC-psbZ LSC 696 0.0284 0.96 69.8 yes View details
rps3-rpl16 LSC 149 0.0537 1.00 69.7 yes View details
ccsA-ndhD SSC 255 0.0431 1.00 69.5 yes View details
ycf3-psaA LSC 753 0.0161 0.99 68.7 yes View details
psbI-psbK LSC 467 0.0257 1.00 68.4 yes View details
psaJ-rps18 LSC 705 0.0128 0.99 66.7 yes View details
rps19-rps3 IRa 579 0.0159 0.98 66.7 no View details
rpoC1-rpoC2 LSC 199 0.0205 0.98 66.2 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps3-rpl16_p1 rps3-rpl16 TGGGATTTTAGGGATAAAAGTTTGG AACGAGTCACACACTAAGCA 210–214 1.000 43.0
rps3-rpl16_p2 rps3-rpl16 ACAGTTCGAACTATTTATGGGA AACGAGTCACACACTAAGCA 227–231 1.000 42.8
rps3-rpl16_p3 rps3-rpl16 ACAGTTCGAACTATTTATGGGA ACGAGTCACACACTAAGCAT 226–230 1.000 42.8
rps3-rpl16_p4 rps3-rpl16 ACAGTTCGAACTATTTATGGGAT AACGAGTCACACACTAAGCA 227–231 1.000 42.8
rps3-rpl16_p5 rps3-rpl16 ACAGTTCGAACTATTTATGGGA AACGAGTCACACACTAAGCAT 227–231 1.000 42.8
ycf3-psaA_p1 ycf3-psaA AAGTTGCGGAGTCTTGGTTT AATGACCAGGTTTTGCCCAT 963–966 1.000 80.8
ycf3-psaA_p2 ycf3-psaA AAGTTGCGGAGTCTTGGTTT ATGACCAGGTTTTGCCCATT 962–965 1.000 80.8
ycf3-psaA_p3 ycf3-psaA TTGGTTGAAGATCACAGGGC AATGACCAGGTTTTGCCCAT 875–878 1.000 80.7
ycf3-psaA_p4 ycf3-psaA TTGGTTGAAGATCACAGGGC ATGACCAGGTTTTGCCCATT 874–877 1.000 80.7
ycf3-psaA_p5 ycf3-psaA AGCTCTTACCCCCGGTAATT ATGACCAGGTTTTGCCCATT 910–913 1.000 80.5
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCCTGAAGGTTGGTCA 823–850 1.000 73.2
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCCTGAAGGTTGGTCAA 823–850 1.000 71.1
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TCTCCTGAAGGTTGGTCAAA 821–848 1.000 69.3
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTCTCCTGAAGGTTGGTCAA 822–849 1.000 69.3
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTCTCCTGAAGGTTGGTCAAA 822–849 1.000 67.5
psbZ-trnS-UGA_p1 psbZ-trnS-UGA TTGACCAACCTTCAGGAGAA CAACCACTCAGCCATCTCTC 490–495 1.000 66.8
psbZ-trnS-UGA_p2 psbZ-trnS-UGA TTTGACCAACCTTCAGGAGA CAACCACTCAGCCATCTCTC 491–496 1.000 66.8
psbZ-trnS-UGA_p3 psbZ-trnS-UGA TTGACCAACCTTCAGGAGAA GTTTTCAAGACCGGGGCTAT 510–515 1.000 65.9
psbZ-trnS-UGA_p4 psbZ-trnS-UGA TTTGACCAACCTTCAGGAGA GTTTTCAAGACCGGGGCTAT 511–516 1.000 65.9
psbZ-trnS-UGA_p5 psbZ-trnS-UGA TTTGACCAACCTTCAGGAGAA CAACCACTCAGCCATCTCTC 491–496 1.000 64.9
trnS-UGA-psbC_p1 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG TCGCGATTTTGAACCTGTTC 334 1.000 75.7
trnS-UGA-psbC_p2 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG CGCGATTTTGAACCTGTTCT 333 1.000 75.7
trnS-UGA-psbC_p3 trnS-UGA-psbC ATAGCCCCGGTCTTGAAAAC TCGCGATTTTGAACCTGTTC 314 1.000 75.1
trnS-UGA-psbC_p4 trnS-UGA-psbC GCTTTTGGAGAGATGGCTGA TCGCGATTTTGAACCTGTTC 341 1.000 74.9
trnS-UGA-psbC_p5 trnS-UGA-psbC AGCTTTTGGAGAGATGGCTG TCGCGATTTTGAACCTGTTC 342 1.000 74.8
psbD-trnT-GGU_p1 psbD-trnT-GGU CCGCAACCAGTCATCCATAA GTGGTAGAGTAACGCCATGG 1125–1143 1.000 81.9
psbD-trnT-GGU_p2 psbD-trnT-GGU CCGCAACCAGTCATCCATAA TCAGTGGTAGAGTAACGCCA 1128–1146 1.000 81.8
psbD-trnT-GGU_p3 psbD-trnT-GGU CACAAAAACGAAACGGTCCC GTGGTAGAGTAACGCCATGG 1146–1164 1.000 80.8
psbD-trnT-GGU_p4 psbD-trnT-GGU CCACAAAAACGAAACGGTCC GTGGTAGAGTAACGCCATGG 1147–1165 1.000 80.8
psbD-trnT-GGU_p5 psbD-trnT-GGU CCCACAAAAACGAAACGGTC GTGGTAGAGTAACGCCATGG 1148–1166 1.000 80.8

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
Phaseolus acutifolius NC_067543.1 150221 View on NCBI ↗
Phaseolus vulgaris NC_009259.1 150285 View on NCBI ↗