Markers + reference

Descurainia

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 153–154 kb
Candidate markers 270
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-CAA LSC 449 0.0303 0.96 67.9 yes View details
rpoB-trnC-UGC LSC 1113 0.0234 1.00 63.9 yes View details
psbM-trnD-GAC LSC 1029 0.0189 0.98 59.3 yes View details
accD LSC 1218 0.0550 1.00 73.4 yes View details
ycf1 IRb 1032 0.0029 1.00 46.7 no View details
ndhF-rpl32 SSC 609 0.0273 0.96 65.2 yes View details
rpl32-trnL-CUA SSC 883 0.0348 0.49 58.3 yes View details
rps15-ycf1 SSC 324 0.0463 1.00 68.4 yes View details
ycf1 SSC 5388 0.0208 1.00 49.5 yes View details
rpl16-rps3 LSC 174 0.0482 0.95 71.8 yes View details
psaA-ycf3 LSC 717 0.0182 1.00 69.3 yes View details
atpH-atpI LSC 502 0.0162 0.98 67.7 yes View details
trnD-GAC-trnY-UAC LSC 438 0.0320 1.00 67.6 yes View details
trnG-GGA-trnR-AGA LSC 161 0.0314 0.99 66.4 yes View details
atpF-atpH LSC 466 0.0172 1.00 65.8 yes View details
rps11-rpl36 LSC 119 0.0336 1.00 65.1 yes View details
trnE-GAA-trnT-ACC LSC 660 0.0228 1.00 64.3 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-CAA_p1 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 502–522 1.000 83.4
rps16-trnQ-CAA_p2 rps16-trnQ-CAA CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 512–532 1.000 82.6
rps16-trnQ-CAA_p3 rps16-trnQ-CAA CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 528–548 1.000 81.0
rps16-trnQ-CAA_p4 rps16-trnQ-CAA TCCACAGCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 529–549 1.000 80.9
rps16-trnQ-CAA_p5 rps16-trnQ-CAA ATCCACAGCAGATCATGTCC GAGGTTCGAATCCTTCCGTC 530–550 1.000 79.2
trnG-GGA-trnR-AGA_p1 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 281–283 1.000 49.1
trnG-GGA-trnR-AGA_p2 trnG-GGA-trnR-AGA ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 287–289 1.000 49.1
trnG-GGA-trnR-AGA_p3 trnG-GGA-trnR-AGA CGACGTCGACTAAAACCCTT TGATATTGCGTCCAATAGGA 301–303 1.000 48.8
trnG-GGA-trnR-AGA_p4 trnG-GGA-trnR-AGA AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 289–291 1.000 48.7
trnG-GGA-trnR-AGA_p5 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 282–284 1.000 48.1
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 584–598 1.000 76.8
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAGTAAACGA TGGCCTGGTTGTAGCATTAG 557–571 1.000 73.5
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TTTATGGCCTGGTTGTAGCA 588–602 1.000 73.0
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCCTGGTTGTAGCATTAGC 583–597 1.000 72.3
atpF-atpH_p5 atpF-atpH GGCCAGTGACCCAAGTAAAC TGGCCTGGTTGTAGCATTAG 559–573 1.000 71.7
atpH-atpI_p1 atpH-atpI TACCTTGACCAACTCCAGGT TACAAGCGGGATTCAAGCTC 664–669 1.000 80.9
atpH-atpI_p2 atpH-atpI GTCCAATAGAAGCAAGCCCA TACAAGCGGGATTCAAGCTC 646–651 1.000 80.9
atpH-atpI_p3 atpH-atpI GCTGTACCTTGACCAACTCC TACAAGCGGGATTCAAGCTC 668–673 1.000 80.3
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCCACTTTAGCTGCG 641–646 1.000 80.2
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTTGCCACTTTAGCTGCG 623–628 1.000 80.1
rpoB-trnC-UGC_p1 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC CCGGATTTGAACTGGGGAAA 1201–1209 1.000 80.2
rpoB-trnC-UGC_p2 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC AAAAGGATTTGCAGTCCCCC 1183–1191 1.000 78.0
rpoB-trnC-UGC_p3 rpoB-trnC-UGC TGTTCCCTCTTTTCCATCCC CCGGATTTGAACTGGGGAAA 1202–1210 1.000 74.1
rpoB-trnC-UGC_p4 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC AAGTCTGTTGTTGAGGCGG 1223–1231 1.000 72.7
rpoB-trnC-UGC_p5 rpoB-trnC-UGC TCTTTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1195–1203 1.000 72.7
psbM-trnD-GAC_p1 psbM-trnD-GAC TGCAAGAATATTGACTTCCA AATTGGTTAGAGCACCGCC 1089–1111 1.000 43.1
psbM-trnD-GAC_p2 psbM-trnD-GAC TGCAAGAATATTGACTTCCA TCAATTGGTTAGAGCACCGC 1091–1113 1.000 43.0
psbM-trnD-GAC_p3 psbM-trnD-GAC ATGCAAGAATATTGACTTCCA TCAATTGGTTAGAGCACCGC 1092–1114 1.000 43.0
psbM-trnD-GAC_p4 psbM-trnD-GAC TGCAAGAATATTGACTTCCAT TCAATTGGTTAGAGCACCGC 1091–1113 1.000 43.0
psbM-trnD-GAC_p5 psbM-trnD-GAC AATGCAAGAATATTGACTTCCA TCAATTGGTTAGAGCACCGC 1093–1115 1.000 43.0

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
Descurainia erodiifolia NC_049625.1 153205 View on NCBI ↗
Descurainia sophia NC_049631.1 154003 View on NCBI ↗