Markers + reference

Lepidium

15 species · Brassicaceae · Brassicales

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Species 15
Genome length 153–155 kb
Candidate markers 266
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-AAA-rps16 LSC 651 0.0404 0.99 78.4 yes View details
trnD-GAC-trnY-UAC LSC 417 0.0444 1.00 72.3 yes View details
trnF-UUC-ndhJ LSC 520 0.0390 0.97 81.6 yes View details
ycf1 IRb 1041 0.0036 1.00 46.6 no View details
ndhF-rpl32 SSC 845 0.0398 0.98 79.5 yes View details
rpl32-trnL-CUA SSC 924 0.0548 0.99 78.9 yes View details
ycf1 SSC 5325 0.0286 1.00 68.8 yes View details
trnE-GAA-trnT-ACC LSC 744 0.0361 0.99 81.2 yes View details
petA-psbJ LSC 896 0.0304 0.99 80.1 yes View details
psbZ-trnG-GGC LSC 479 0.0320 1.00 78.9 yes View details
ndhC-trnV-GUA LSC 566 0.0339 1.00 78.2 yes View details
trnS-AGC-trnG-GGA LSC 632 0.0354 0.99 77.9 yes View details
psbM-trnD-GAC LSC 1025 0.0306 0.99 76.8 yes View details
trnT-ACC-psbD LSC 1179 0.0219 1.00 76.7 yes View details
trnG-GGA-trnR-AGA LSC 154 0.0523 0.99 76.1 yes View details
rps16 LSC 1118 0.0221 1.00 76.0 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-AAA-rps16_p1 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG ATCTTCGCAAGGTGGGTTTT 889–1009 1.000 91.8
trnK-AAA-rps16_p2 trnK-AAA-rps16 GCGGATCTGGACGAATTCTT ATCTTCGCAAGGTGGGTTTT 853–973 0.867 86.2
trnK-AAA-rps16_p3 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 949–1069 0.867 86.1
trnK-AAA-rps16_p4 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 950–1070 0.867 86.1
trnK-AAA-rps16_p5 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG GGTTTGTTGCTGCCCTTTTT 1417–1543 0.733 80.0
rps16_p1 rps16 ACGAGTCTTTCACATCCTCT TCAATTACACAAACTAGAGGAATGT 1154–1226 1.000 51.0
rps16_p2 rps16 AGAGGAGGAAAGCAAAGAGT TCAATTACACAAACTAGAGGAATGT 1200–1264 0.933 47.0
rps16_p3 rps16 AAGAGGAGGAAAGCAAAGAGT TCAATTACACAAACTAGAGGAATGT 1201–1265 0.933 47.0
rps16_p4 rps16 AGAGGAGGAAAGCAAAGAGT TGAATCAATTACACAAACTAGAGGA 1204–1268 0.933 47.0
rps16_p5 rps16 AGAGGAGGAAAGCAAAGAGT CAATTACACAAACTAGAGGAATGT 1199–1263 0.933 47.0
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA ACGAATCACACTTTTACCACT 685–730 1.000 62.4
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC ACGAATCACACTTTTACCACT 683–728 1.000 62.1
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GAACGAATCACACTTTTACCACT 687–732 1.000 61.3
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC GAACGAATCACACTTTTACCACT 685–730 1.000 61.0
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AACGAATCACACTTTTACCACT 686–731 1.000 60.5
trnG-GGA-trnR-AGA_p1 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 258–292 1.000 58.6
trnG-GGA-trnR-AGA_p2 trnG-GGA-trnR-AGA ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 264–298 1.000 58.4
trnG-GGA-trnR-AGA_p3 trnG-GGA-trnR-AGA AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 266–300 1.000 58.0
trnG-GGA-trnR-AGA_p4 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 259–293 1.000 57.6
trnG-GGA-trnR-AGA_p5 trnG-GGA-trnR-AGA ACCCTTAGCCTTCCAAGCTA TTGATATTGCGTCCAATAGGA 265–299 1.000 57.4
psbM-trnD-GAC_p1 psbM-trnD-GAC GAGAATGAAGAGTGCAGTAGC GTTCGAGCCCCGTCAGTC 1069–1102 1.000 52.0
psbM-trnD-GAC_p2 psbM-trnD-GAC AGAATGAAGAGTGCAGTAGC GTTCGAGCCCCGTCAGTC 1068–1101 1.000 52.0
psbM-trnD-GAC_p3 psbM-trnD-GAC GAGAATGAAGAGTGCAGTAGC GAGCACCGCCCTGTCAAG 1100–1133 1.000 52.0
psbM-trnD-GAC_p4 psbM-trnD-GAC GAGAATGAAGAGTGCAGTAGC GCCCTGTCAAGGCGGAAG 1093–1126 1.000 52.0
psbM-trnD-GAC_p5 psbM-trnD-GAC AGAATGAAGAGTGCAGTAGC GAGCACCGCCCTGTCAAG 1099–1132 1.000 52.0
trnD-GAC-trnY-UAC_p1 trnD-GAC-trnY-UAC ACCAATTGAACTACAATCCC TGGCAATATGTCTACGCTGG 477–511 0.867 46.2
trnD-GAC-trnY-UAC_p2 trnD-GAC-trnY-UAC ACCAATTGAACTACAATCCC GGCAATATGTCTACGCTGGT 476–510 0.867 46.2
trnD-GAC-trnY-UAC_p3 trnD-GAC-trnY-UAC ACCAATTGAACTACAATCCC GGGGACGGACTGTAAATTCG 498–532 0.867 46.1
trnD-GAC-trnY-UAC_p4 trnD-GAC-trnY-UAC ACCAATTGAACTACAATCCC GGGACGGACTGTAAATTCGT 497–531 0.867 46.1
trnD-GAC-trnY-UAC_p5 trnD-GAC-trnY-UAC ACCAATTGAACTACAATCCC GATTCTTCCTGGGTCGATGC 531–565 0.867 45.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Lepidium appelianum NC_077510.1 153803 View on NCBI ↗
Lepidium campestre PV712666.1 154145 View on NCBI ↗
Lepidium cartilagineum NC_077509.1 153991 View on NCBI ↗
Lepidium chalepense NC_077508.1 153810 View on NCBI ↗
Lepidium cordatum NC_077507.1 153177 View on NCBI ↗
Lepidium cuneiforme PV712664.1 154942 View on NCBI ↗
Lepidium densiflorum PV712663.1 154622 View on NCBI ↗
Lepidium didymum PV712662.1 154851 View on NCBI ↗
Lepidium draba NC_077506.1 153675 View on NCBI ↗
Lepidium echinatum NC_049660.1 154504 View on NCBI ↗
Lepidium ferganense NC_077505.1 154754 View on NCBI ↗
Lepidium latifolium NC_053830.1 153989 View on NCBI ↗
Lepidium meyenii NC_034363.1 154403 View on NCBI ↗
Lepidium perfoliatum NC_049663.1 154414 View on NCBI ↗
Lepidium virginicum NC_009273.1 154743 View on NCBI ↗