Markers + reference

Parrya

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 157–161 kb
Candidate markers 259
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhA SSC 2172 0.4099 0.89 80.6 yes View details
ndhI SSC 504 0.4442 0.80 77.4 yes View details
ndhG SSC 543 0.4512 0.60 72.9 yes View details
ndhD SSC 1443 0.4551 0.83 80.3 yes View details
trnL-UAG-ndhF SSC 1594 0.4379 0.73 77.1 yes View details
ndhF SSC 2241 0.4882 0.83 78.8 yes View details
rbcL-accD LSC 951 0.1025 0.93 83.7 yes View details
accD LSC 1704 0.0944 0.95 81.9 yes View details
ccsA SSC 981 0.4415 0.81 79.7 yes View details
psaJ-rpl33 LSC 432 0.0605 0.96 78.6 yes View details
ndhG-ndhE SSC 237 0.4267 0.95 77.3 yes View details
ndhD-ccsA SSC 223 0.4095 0.94 77.3 yes View details
ndhE-psaC SSC 241 0.4978 0.93 76.6 yes View details
trnN-GUU-rps15 IRb 6320 0.0366 0.97 76.4 yes View details
rps15-trnN-GUU IRa 6320 0.0366 0.97 76.4 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rbcL-accD_p1 rbcL-accD TTGAATGCTACTGCGGGTAC GTTTCCTCCAGCTTCTCGAG 2252 0.500 59.8
rbcL-accD_p2 rbcL-accD TGCAATGCACGCTGTTATTG GTTTCCTCCAGCTTCTCGAG 2085 0.500 59.8
rbcL-accD_p3 rbcL-accD TCATGGTATGCACTTCCGTG GTTTCCTCCAGCTTCTCGAG 2052 0.500 59.8
rbcL-accD_p4 rbcL-accD AATGAGGGACGTGATCTTGC GTTTCCTCCAGCTTCTCGAG 1676 0.500 59.7
rbcL-accD_p5 rbcL-accD CTTAACAGGGGGATTCACCG GTTTCCTCCAGCTTCTCGAG 2163 0.500 59.7
accD_p1 accD CCGCCAGTAATAATCCCAGG GGAGGTACAAGCAAAGACCA 2341 0.500 54.0
accD_p2 accD ATGCCGCCAGTAATAATCCC GGAGGTACAAGCAAAGACCA 2344 0.500 53.9
accD_p3 accD GGGATGCCGCCAGTAATAAT GGAGGTACAAGCAAAGACCA 2347 0.500 53.9
accD_p4 accD AATCTTAGCCGTTGCATCGA GGAGGTACAAGCAAAGACCA 2817 0.500 53.0
accD_p5 accD CCGCCAGTAATAATCCCAGG CCTTTGAACTTCCCGAAAGC 1957 0.500 52.9
psaJ-rpl33_p1 psaJ-rpl33 TCCAGATGCATTAACATTTCCCT CGAACATCTTTACCCTTTGCC 477–486 1.000 50.4
psaJ-rpl33_p2 psaJ-rpl33 TCCAGATGCATTAACATTTCCC CGAACATCTTTACCCTTTGCC 477–486 1.000 49.2
psaJ-rpl33_p3 psaJ-rpl33 CCAGATGCATTAACATTTCCCT CGAACATCTTTACCCTTTGCC 476–485 1.000 49.2
psaJ-rpl33_p4 psaJ-rpl33 TTCCAGATGCATTAACATTTCCC CGAACATCTTTACCCTTTGCC 478–487 1.000 47.3
psaJ-rpl33_p5 psaJ-rpl33 CCAGATGCATTAACATTTCCCTT CGAACATCTTTACCCTTTGCC 476–485 1.000 47.3
trnN-GUU-rps15_p1 trnN-GUU-rps15 CCCGGAACTTCTTCGTAGTG ACGAACATCATGAGCTGTCC 587–702 1.000 84.5
trnN-GUU-rps15_p2 trnN-GUU-rps15 CCCGGAACTTCTTCGTAGTG GGAAGAGATAAGAGGGCCCT 484–599 1.000 84.2
trnN-GUU-rps15_p3 trnN-GUU-rps15 CGTAGTGTCTCCGTTCCATG ACGAACATCATGAGCTGTCC 574–689 1.000 84.0
trnN-GUU-rps15_p4 trnN-GUU-rps15 CCCGGAACTTCTTCGTAGTG CGTGTTGTTGCATCGAAACA 861–976 1.000 83.9
trnN-GUU-rps15_p5 trnN-GUU-rps15 CAATTCCCGTTCTCAACCCA ACGAACATCATGAGCTGTCC 641–756 1.000 83.6
ndhA_p1 ndhA AGTTGAAGCTCCAAAAGGGG CAGCTCGTAGGGTTTGTTGA 2508 0.500 58.7
ndhA_p2 ndhA AGTTGAAGCTCCAAAAGGGG AGCTCGTAGGGTTTGTTGAC 2507 0.500 58.7
ndhA_p3 ndhA GTTGAAGCTCCAAAAGGGGA CAGCTCGTAGGGTTTGTTGA 2507 0.500 58.7
ndhA_p4 ndhA GTTGAAGCTCCAAAAGGGGA AGCTCGTAGGGTTTGTTGAC 2506 0.500 58.6
ndhA_p5 ndhA AGTTGAAGCTCCAAAAGGGG CCAATATACCTGGCAGCTCG 2521 0.500 58.4
ndhI_p1 ndhI ATTTGTGGCGTCAACCGATA GTGCAGCAGCTACAAAATGG 1554 0.500 59.1
ndhI_p2 ndhI ATTTGTGGCGTCAACCGATA CCATTCCCAACGGTCCATAG 1663 0.500 58.9
ndhI_p3 ndhI ATTTGTGGCGTCAACCGATA GCCCCCACGTAAATAAGGAG 1576 0.500 58.9
ndhI_p4 ndhI ATTTGTGGCGTCAACCGATA TAACCCCGTACCATGACGTA 1740 0.500 58.1
ndhI_p5 ndhI ATTTGTGGCGTCAACCGATA GTTTATGGCCCCCACGTAAA 1583 0.500 57.9

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
Parrya alba PZ101455.1 160925 View on NCBI ↗
Parrya pinnatifida MK637777.1 156873 View on NCBI ↗