Markers + reference

Murraya

4 species · Rutaceae · Sapindales

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Species 4
Genome length 158–160 kb
Candidate markers 243
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 243 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GTG-psbA LSC 448 0.0360 0.97 70.7 yes View details
matK-rps16 LSC 1374 0.0241 0.94 65.6 yes View details
rps16-trnQ-TTG LSC 1275 0.0289 0.83 68.7 yes View details
trnS-GCT-trnR-TCT LSC 1826 0.0293 0.99 72.8 yes View details
atpF-atpH LSC 491 0.0439 0.94 75.2 yes View details
petN-psbM LSC 1286 0.0305 0.98 71.3 yes View details
trnS-TGA-psbZ LSC 355 0.0315 0.98 57.8 yes View details
petA-psbJ LSC 1103 0.0237 0.97 71.2 yes View details
ndhF SSC 2229 0.0152 1.00 53.2 yes View details
ndhF-rpl32 SSC 1024 0.0299 0.94 68.5 yes View details
rpl32-trnL-TAG SSC 471 0.0343 0.96 70.2 yes View details
ccsA-ndhD SSC 370 0.0471 0.83 75.5 yes View details
ycf1 SSC 5544 0.0188 0.99 53.7 yes View details
trnL-TAG-ccsA SSC 111 0.0556 0.92 75.7 yes View details
trnD-GTC-trnY-GTA LSC 486 0.0293 0.96 74.0 yes View details
psaC-ndhE SSC 235 0.0376 1.00 70.5 yes View details
psaJ-rpl33 LSC 492 0.0259 0.98 69.5 yes View details
psbC-trnS-TGA LSC 254 0.0296 0.95 68.9 yes View details
ndhI-ndhA SSC 88 0.0458 0.91 68.1 yes View details
ycf4-cemA LSC 744 0.0214 0.97 67.9 yes View details
atpB-rbcL LSC 787 0.0135 0.99 67.6 yes View details
rpl36-rps8 LSC 403 0.0282 0.98 66.3 yes View details
trnT-GGT-psbD LSC 1248 0.0257 0.99 66.0 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GTG-psbA_p1 trnH-GTG-psbA GATCCACTTGGCTACATCCG TGAAGCCCCATCTACAAATGG 494–523 1.000 77.4
trnH-GTG-psbA_p2 trnH-GTG-psbA CAATCCACTGCCTTGATCCA TGAAGCCCCATCTACAAATGG 508–537 1.000 77.2
trnH-GTG-psbA_p3 trnH-GTG-psbA AATCCACTGCCTTGATCCAC TGAAGCCCCATCTACAAATGG 507–536 1.000 77.2
trnH-GTG-psbA_p4 trnH-GTG-psbA ACAATCCACTGCCTTGATCC TGAAGCCCCATCTACAAATGG 509–538 1.000 77.1
trnH-GTG-psbA_p5 trnH-GTG-psbA CGCATGGTGGATTCACAATC TGAAGCCCCATCTACAAATGG 523–552 1.000 74.2
matK-rps16_p1 matK-rps16 CCTTCCAATGGCATCATCGA CCCAATGAGCCGTTTATCGA 1684–1744 1.000 86.3
matK-rps16_p2 matK-rps16 CCTTCCAATGGCATCATCGA GGTGTGTTGCTGCCATTTTT 2161–2236 1.000 85.9
matK-rps16_p3 matK-rps16 AGAGGCATCCTTTACCCAGT CCCAATGAGCCGTTTATCGA 2063–2123 1.000 85.5
matK-rps16_p4 matK-rps16 AGAGGCATCCTTTACCCAGT TCCCAATGAGCCGTTTATCG 2064–2124 1.000 85.5
matK-rps16_p5 matK-rps16 AGAGGCATCCTTTACCCAGT GGTGTGTTGCTGCCATTTTT 2540–2615 1.000 85.3
rps16-trnQ-TTG_p1 rps16-trnQ-TTG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1170–1366 1.000 87.0
rps16-trnQ-TTG_p2 rps16-trnQ-TTG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1168–1364 1.000 87.0
rps16-trnQ-TTG_p3 rps16-trnQ-TTG CAGCGGATCATGTCCTTCAA CGAAATTGAAATGGGGCGTC 1229–1425 1.000 86.7
rps16-trnQ-TTG_p4 rps16-trnQ-TTG CAGCGGATCATGTCCTTCAA GAAATTGAAATGGGGCGTCG 1228–1424 1.000 86.7
rps16-trnQ-TTG_p5 rps16-trnQ-TTG GCGGATCATGTCCTTCAAGT GAAATTGAAATGGGGCGTCG 1226–1422 1.000 86.7
trnS-GCT-trnR-TCT_p1 trnS-GCT-trnR-TCT CCGACGCTTTAATCCACTCA AGAAGACCTCTGTCCTATCCA 1893–1963 1.000 68.5
trnS-GCT-trnR-TCT_p2 trnS-GCT-trnR-TCT CCGACGCTTTAATCCACTCA AGGTTTAGAAGACCTCTGTCCT 1899–1969 1.000 67.8
trnS-GCT-trnR-TCT_p3 trnS-GCT-trnR-TCT ACGGAAAGAGAGGGATTCGA AGAAGACCTCTGTCCTATCCA 1951–2021 1.000 67.2
trnS-GCT-trnR-TCT_p4 trnS-GCT-trnR-TCT ACGGAAAGAGAGGGATTCGA AGGTTTAGAAGACCTCTGTCCT 1957–2027 1.000 66.5
trnS-GCT-trnR-TCT_p5 trnS-GCT-trnR-TCT ACGCTTTAATCCACTCAGCC AGAAGACCTCTGTCCTATCCA 1890–1960 1.000 66.5
atpF-atpH_p1 atpF-atpH TGGGTCCAGCCTATTCTTGA ATTTCTGCCGCTTCCGTTAT 880–906 1.000 86.1
atpF-atpH_p2 atpF-atpH CCAACAAATCGCGAAATGCT ATTTCTGCCGCTTCCGTTAT 1002–1022 1.000 85.6
atpF-atpH_p3 atpF-atpH CAGCATAAAAGGGGGTTGGT ATTTCTGCCGCTTCCGTTAT 1300–1320 1.000 84.6
atpF-atpH_p4 atpF-atpH CCAACAAATCGCGAAATGCT GTGTCTGTGGATCGAAACGA 1245 0.250 49.4
atpF-atpH_p5 atpF-atpH TGGGTCCAGCCTATTCTTGA GTGTCTGTGGATCGAAACGA 1129 0.250 49.2
petN-psbM_p1 petN-psbM ATGGGGAAGAAGTGGACTCT AAAACGGTCAGTCAAAGTGA 1317–1354 1.000 64.6
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT AAAAACGGTCAGTCAAAGTGA 1318–1355 1.000 62.9
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT AAACGGTCAGTCAAAGTGAT 1316–1353 1.000 62.7
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT AACGGTCAGTCAAAGTGATT 1315–1352 1.000 62.7
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT AAACGGTCAGTCAAAGTGATT 1316–1353 1.000 61.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Murraya koenigii NC_032684.1 159402 View on NCBI ↗
Murraya paniculata NC_052700.1 160280 View on NCBI ↗
Murraya paniculata var. omphalocarpa LC849113.1 160074 View on NCBI ↗
Murraya sumatrana LC858458.1 158427 View on NCBI ↗