Markers + reference

Gastrolobium

2 species · Fabaceae · Fabales

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Species 2
Genome length 151–151 kb
Candidate markers 260
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

2 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 4716 0.0546 1.00 68.0 yes View details
ycf1-trnN-GUU SSC 997 0.0373 0.97 68.9 yes View details
rpl2-rpl23 IRb 18 0.0556 1.00 81.9 yes View details
rpl23-rpl2 IRa 18 0.0556 1.00 81.9 yes View details
ndhG-ndhI SSC 396 0.0840 0.93 77.2 yes View details
ndhF-rpl32 SSC 485 0.0684 0.96 76.9 yes View details
trnL-UAG-ccsA SSC 118 0.0521 0.81 73.2 yes View details
rps15-ycf1 SSC 338 0.0590 0.90 71.0 yes View details
rpl32-trnL-UAG SSC 268 0.0709 1.00 69.1 yes View details
rpl32 SSC 177 0.0508 1.00 67.3 yes View details
ndhA SSC 2387 0.0328 0.97 66.6 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl2-rpl23_p1 rpl2-rpl23 CACTTGACTGTCTACGGCTC GTAAAGGGTAGAAGGGTGCG 198 1.000 80.1
rpl2-rpl23_p2 rpl2-rpl23 CCACAACGATGCTGTCCATA GTAAAGGGTAGAAGGGTGCG 245 1.000 80.0
rpl2-rpl23_p3 rpl2-rpl23 CACTTGACTGTCTACGGCTC TAAAGGGTAGAAGGGTGCGA 197 1.000 79.8
rpl2-rpl23_p4 rpl2-rpl23 CCACAACGATGCTGTCCATA TAAAGGGTAGAAGGGTGCGA 244 1.000 79.7
rpl2-rpl23_p5 rpl2-rpl23 GACTGTCTACGGCTCCATTG GTAAAGGGTAGAAGGGTGCG 193 1.000 79.7
ndhF-rpl32_p1 ndhF-rpl32 ACACACTCCAACCAATTCCC CGAGAAAATTCCGCGAATCG 1168 0.500 59.9
ndhF-rpl32_p2 ndhF-rpl32 CACACTCCAACCAATTCCCA CGAGAAAATTCCGCGAATCG 1167 0.500 59.9
ndhF-rpl32_p3 ndhF-rpl32 ACCAATCCCAACATTGCAGT CGAGAAAATTCCGCGAATCG 1113 0.500 59.8
ndhF-rpl32_p4 ndhF-rpl32 CCACAGGAAACAGCAGAAGT CGAGAAAATTCCGCGAATCG 791 0.500 59.7
ndhF-rpl32_p5 ndhF-rpl32 GCAACCGAACCGCAAAATAA CGAGAAAATTCCGCGAATCG 1413 0.500 59.5
rpl32_p1 rpl32 CCACAGGAAACAGCAGAAGT AAGCACGGAACCATGTGAAT 1494–1524 1.000 84.7
rpl32_p2 rpl32 CCACAGGAAACAGCAGAAGT GATAAGATGCCATGCCGCTA 1116–1168 1.000 84.5
rpl32_p3 rpl32 CCACAGGAAACAGCAGAAGT ACGGAACCATGTGAATGAGG 1490–1520 1.000 84.5
rpl32_p4 rpl32 CCACAGGAAACAGCAGAAGT TCCTAAGAGCAGCGTGTCTA 1063–1115 1.000 84.5
rpl32_p5 rpl32 CCACAGGAAACAGCAGAAGT CGAGAAAATTCCGCGAATCG 791 0.500 59.7
rpl32-trnL-UAG_p1 rpl32-trnL-UAG TGGACAGCACTGAAAGCTTT AAGTTGCAAAGGCTTGGGTA 917–937 1.000 84.0
rpl32-trnL-UAG_p2 rpl32-trnL-UAG TGGACAGCACTGAAAGCTTT AGTTGCAAAGGCTTGGGTAA 916–936 1.000 84.0
rpl32-trnL-UAG_p3 rpl32-trnL-UAG TTGGACAGCACTGAAAGCTT AAGTTGCAAAGGCTTGGGTA 918–938 1.000 84.0
rpl32-trnL-UAG_p4 rpl32-trnL-UAG TTGGACAGCACTGAAAGCTT AGTTGCAAAGGCTTGGGTAA 917–937 1.000 84.0
rpl32-trnL-UAG_p5 rpl32-trnL-UAG TGGACAGCACTGAAAGCTTT AAGCACGGAACCATGTGAAT 840–860 1.000 84.0
trnL-UAG-ccsA_p1 trnL-UAG-ccsA TAGACACGCTGCTCTTAGGA CGATCGAAAACGATAGATGGG 209–231 1.000 66.3
trnL-UAG-ccsA_p2 trnL-UAG-ccsA TAGACACGCTGCTCTTAGGA ACGATCGAAAACGATAGATGGG 210–232 1.000 65.9
trnL-UAG-ccsA_p3 trnL-UAG-ccsA TAGACACGCTGCTCTTAGGA CGATCGAAAACGATAGATGGGT 209–231 1.000 65.9
trnL-UAG-ccsA_p4 trnL-UAG-ccsA AAATTGGTAGACACGCTGCT CGATCGAAAACGATAGATGGG 216–238 1.000 65.8
trnL-UAG-ccsA_p5 trnL-UAG-ccsA GTAGACACGCTGCTCTTAGG CGATCGAAAACGATAGATGGG 210–232 1.000 65.7
ndhG-ndhI_p1 ndhG-ndhI ATGTAGCGATTCGGGCAAAT TCAACAAACAATCCGAGCCA 855–871 1.000 85.4
ndhG-ndhI_p2 ndhG-ndhI ATGTAGCGATTCGGGCAAAT CAACAAACAATCCGAGCCAC 854–870 1.000 85.2
ndhG-ndhI_p3 ndhG-ndhI GTGCTGCAGCTACAAAATGG TCAACAAACAATCCGAGCCA 1015–1031 1.000 84.8
ndhG-ndhI_p4 ndhG-ndhI GTGCTGCAGCTACAAAATGG CAACAAACAATCCGAGCCAC 1014–1030 1.000 84.7
ndhG-ndhI_p5 ndhG-ndhI AACAAACGCTCTTTCACCCT TCAACAAACAATCCGAGCCA 1480 0.500 59.4

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
Gastrolobium bilobum PP920093.1 151465 View on NCBI ↗
Gastrolobium praemorsum PV870803.1 151178 View on NCBI ↗