Markers + reference

Robinia

2 species · Fabaceae · Fabales

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Species 2
Genome length 155–155 kb
Candidate markers 260
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL LSC 602 0.0257 0.97 63.3 yes View details
trnV-UAC-ndhC LSC 413 0.0410 0.89 76.2 yes View details
rps4-trnS-GGA LSC 229 0.0175 1.00 52.7 yes View details
trnS-GGA-trnG-GCC LSC 758 0.0218 0.97 69.1 yes View details
atpH-atpI LSC 1383 0.0154 0.98 55.0 yes View details
trnT-GGU-psbD LSC 1443 0.0147 0.99 64.5 yes View details
psaA-ycf3 LSC 860 0.0245 1.00 72.8 yes View details
ycf3 LSC 1967 0.0122 1.00 52.3 yes View details
trnQ-UUG-accD LSC 1344 0.0240 0.99 64.3 yes View details
psbE-petL LSC 1370 0.0156 0.98 56.9 yes View details
trnP-UGG-psaJ LSC 458 0.0111 0.98 56.4 yes View details
rps3-rpl2 LSC 771 0.0259 1.00 69.2 yes View details
ndhF SSC 2247 0.0116 1.00 57.8 yes View details
ycf1 SSC 5337 0.0139 1.00 47.4 yes View details
rpl2-trnH-GUG IRa 101 0.0928 0.96 82.8 no View details
trnW-CCA-trnP-UGG LSC 196 0.0510 1.00 76.7 yes View details
trnF-GAA-trnL-UAA LSC 390 0.0359 1.00 71.7 yes View details
rpl36-rps8 LSC 440 0.0250 1.00 69.8 yes View details
psbT-psbN LSC 66 0.0606 1.00 68.7 yes View details
petA-psbJ LSC 1213 0.0124 0.99 66.5 yes View details
accD-psaI LSC 452 0.0244 1.00 65.0 yes View details
psbZ-trnG-UCC LSC 738 0.0178 0.76 64.9 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rbcL_p1 trnK-UUU-rbcL AGCCGAGTACTCTACCATTGA GAATTCCCAGCAATGGATAC 661–1083 1.000 43.7
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AATGGAGTCGCGCTTAAAAG GAATTCCCAGCAATGGATAC 679–1101 1.000 43.0
trnK-UUU-rbcL_p3 trnK-UUU-rbcL GCCGAGTACTCTACCATTGAG GAATTCCCAGCAATGGATAC 660–1082 1.000 43.0
trnK-UUU-rbcL_p4 trnK-UUU-rbcL AAATGGAGTCGCGCTTAAAAG GAATTCCCAGCAATGGATAC 680–1102 1.000 43.0
trnK-UUU-rbcL_p5 trnK-UUU-rbcL GCCGAGTACTCTACCATTGA GAATTCCCAGCAATGGATAC 660–1082 1.000 43.0
trnV-UAC-ndhC_p1 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT CCTTTGCTAATCGGGGCTAA 536–556 1.000 81.9
trnV-UAC-ndhC_p2 trnV-UAC-ndhC GAAGGTCTACGGTTCGAGTC CCTTTGCTAATCGGGGCTAA 535–555 1.000 79.1
trnV-UAC-ndhC_p3 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT CTCTGGCCCTTTGCTAATCG 543–563 1.000 79.0
trnV-UAC-ndhC_p4 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT TCTCTGGCCCTTTGCTAATC 544–564 1.000 78.8
trnV-UAC-ndhC_p5 trnV-UAC-ndhC CGGTTCGAGTCCGTATAGTC CCTTTGCTAATCGGGGCTAA 526–546 1.000 78.2
trnF-GAA-trnL-UAA_p1 trnF-GAA-trnL-UAA TCTACCAGCTGAGCTATCCC AATCGTGAGGGTTCAAGTCC 444 1.000 78.7
trnF-GAA-trnL-UAA_p2 trnF-GAA-trnL-UAA TTTGAACTGGTGACACGAGG AATCGTGAGGGTTCAAGTCC 480 1.000 78.1
trnF-GAA-trnL-UAA_p3 trnF-GAA-trnL-UAA GTGCCAGGAACCAGATTTGA AATCGTGAGGGTTCAAGTCC 495 1.000 77.7
trnF-GAA-trnL-UAA_p4 trnF-GAA-trnL-UAA TCAGTCCTCTGCTCTACCAG AATCGTGAGGGTTCAAGTCC 456 1.000 77.6
trnF-GAA-trnL-UAA_p5 trnF-GAA-trnL-UAA CATGTGCCAGGAACCAGATT AATCGTGAGGGTTCAAGTCC 498 1.000 77.2
rps4-trnS-GGA_p1 rps4-trnS-GGA GCTGGTTGTAGAATATTATTCTCGC TGGACTAAAGCGTCGGATTG 335 1.000 41.0
rps4-trnS-GGA_p2 rps4-trnS-GGA TGGTTGTAGAATATTATTCTCGCCA TGGACTAAAGCGTCGGATTG 333 1.000 41.0
rps4-trnS-GGA_p3 rps4-trnS-GGA GCTGGTTGTAGAATATTATTCTCGC GTGGACTAAAGCGTCGGATT 336 1.000 41.0
rps4-trnS-GGA_p4 rps4-trnS-GGA TGGTTGTAGAATATTATTCTCGCCA GTGGACTAAAGCGTCGGATT 334 1.000 41.0
rps4-trnS-GGA_p5 rps4-trnS-GGA TGAATTGCTGGTTGTAGAAT TGGACTAAAGCGTCGGATTG 341 1.000 40.9
trnS-GGA-trnG-GCC_p1 trnS-GGA-trnG-GCC CAATCCGACGCTTTAGTCCA GGGTCTATACAACGAATCGCA 818–838 1.000 75.2
trnS-GGA-trnG-GCC_p2 trnS-GGA-trnG-GCC AATCCGACGCTTTAGTCCAC GGGTCTATACAACGAATCGCA 817–837 1.000 75.2
trnS-GGA-trnG-GCC_p3 trnS-GGA-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 807–827 1.000 74.1
trnS-GGA-trnG-GCC_p4 trnS-GGA-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 806–826 1.000 74.1
trnS-GGA-trnG-GCC_p5 trnS-GGA-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 807–827 1.000 74.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GAATATGGTCCGTGGGTTCC 1892–1927 1.000 81.3
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTGGTCAGGGGCTCTTTTG 1834–1869 1.000 81.1
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT CGCAAACCATTCCCACTTTC 1978–2013 1.000 81.0
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT GCAAACCATTCCCACTTTCG 1977–2012 1.000 81.0
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAAATCCGCAAACCATTCC 1985–2020 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
Robinia neomexicana var. luxurians PQ834960.1 154579 View on NCBI ↗
Robinia pseudoacacia NC_026684.1 154835 View on NCBI ↗