Markers + reference

Murbeckiella

2 species · Brassicaceae · Brassicales

Back to catalogue

Species 2
Genome length 155–155 kb
Candidate markers 270
Primer pairs 95

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
psbA LSC 1062 0.0000 1.00 29.3 yes View details
trnK-AAA-rps16 LSC 648 0.0141 0.98 68.3 yes View details
rpoB-trnC-UGC LSC 1089 0.0046 1.00 61.8 yes View details
trnC-UGC-petN LSC 662 0.0031 0.98 62.9 yes View details
psbM-trnD-GAC LSC 1002 0.0060 1.00 62.2 yes View details
trnD-GAC-trnY-UAC LSC 426 0.0023 1.00 53.5 yes View details
rbcL-accD LSC 691 0.0145 1.00 67.5 yes View details
psaJ-rpl33 LSC 429 0.0210 1.00 63.9 yes View details
ndhF-rpl32 SSC 837 0.0060 1.00 62.3 yes View details
trnM-AUG-atpE LSC 139 0.0360 1.00 73.2 yes View details
trnH-CAC-psbA LSC 246 0.0244 1.00 66.5 yes View details
psbI-trnS-AGC LSC 91 0.0220 1.00 65.1 yes View details
trnE-GAA-trnT-ACC LSC 820 0.0037 0.99 62.2 yes View details
trnR-CGU-trnN-AAC IRb 630 0.0048 1.00 61.5 yes View details
trnN-AAC-trnR-CGU IRa 630 0.0048 1.00 61.5 yes View details
rps4-trnT-ACA LSC 407 0.0026 0.95 61.0 yes View details
rpl20-rps12 LSC 753 0.0040 1.00 61.0 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 304–307 1.000 80.1
trnH-CAC-psbA_p2 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 319–322 1.000 79.9
trnH-CAC-psbA_p3 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 305–308 1.000 79.9
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 322–325 1.000 79.8
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 320–323 1.000 79.7
psbA_p1 psbA AGAAGGCGTATATTGCTCGT AGAATTTGTGCGCTTGGGA 1171 1.000 62.3
psbA_p2 psbA AGAAGGCGTATATTGCTCGT AGAATTTGTGCGCTTGGGAG 1171 1.000 61.6
psbA_p3 psbA AGAAGGCGTATATTGCTCGT AGAGAATTTGTGCGCTTGGG 1173 1.000 61.6
psbA_p4 psbA AGAAGGCGTATATTGCTCGT GAGAATTTGTGCGCTTGGGA 1172 1.000 61.6
psbA_p5 psbA AGAAGGCGTATATTGCTCGT GCTTGGGAGTCCCTGATGAT 1160 1.000 61.3
trnK-AAA-rps16_p1 trnK-AAA-rps16 AACTCTACCGCAGATCTGGA AAGGCAGGGATTTTTACGGA 791–801 1.000 73.6
trnK-AAA-rps16_p2 trnK-AAA-rps16 AACTCTACCGCAGATCTGGA AGGCAGGGATTTTTACGGAA 790–800 1.000 73.6
trnK-AAA-rps16_p3 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT AGGCAGGGATTTTTACGGAA 722–732 1.000 73.6
trnK-AAA-rps16_p4 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT AAGGCAGGGATTTTTACGGA 722–732 1.000 73.6
trnK-AAA-rps16_p5 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT AGGCAGGGATTTTTACGGAA 721–731 1.000 73.6
psbI-trnS-AGC_p1 psbI-trnS-AGC TCCTATCTAATGATCCAGGACGT TAGGAGAGATGGCTGAGTGG 225 1.000 56.1
psbI-trnS-AGC_p2 psbI-trnS-AGC TCCTATCTAATGATCCAGGACGT GGCTGAGTGGATTAAAGCGT 215 1.000 54.7
psbI-trnS-AGC_p3 psbI-trnS-AGC TCCTATCTAATGATCCAGGACGT TGGCTGAGTGGATTAAAGCG 216 1.000 54.6
psbI-trnS-AGC_p4 psbI-trnS-AGC TCCTATCTAATGATCCAGGACGT CGAGTTAATCGTACCGAGGG 175 1.000 53.7
psbI-trnS-AGC_p5 psbI-trnS-AGC CCTATCTAATGATCCAGGACGT TAGGAGAGATGGCTGAGTGG 224 1.000 52.8
trnG-GGA_p1 trnG-GGA ACCCCCGATTACTTTGTTCG AAAAAGGGGCAATTGTGAAT 868–869 1.000 48.7
trnG-GGA_p2 trnG-GGA ACCCCCGATTACTTTGTTCG AAAAGGGGCAATTGTGAATT 867–868 1.000 48.7
trnG-GGA_p3 trnG-GGA ACCCCCGATTACTTTGTTCG AAAGGGGCAATTGTGAATTT 866–867 1.000 48.7
trnG-GGA_p4 trnG-GGA ACCCCCGATTACTTTGTTCG AAAAAGGGGCAATTGTGAATT 868–869 1.000 47.7
trnG-GGA_p5 trnG-GGA ACCCCCGATTACTTTGTTCG AAAAGGGGCAATTGTGAATTT 867–868 1.000 47.7
rpoB-trnC-UGC_p1 rpoB-trnC-UGC CCGGGTATTGTAGATGTTCCC CCGGATTTGAACTGGGGAAA 1189–1192 1.000 71.0
rpoB-trnC-UGC_p2 rpoB-trnC-UGC GTTCCCTCTTTTTCATCCCCA CCGGATTTGAACTGGGGAAA 1174–1177 1.000 70.6
rpoB-trnC-UGC_p3 rpoB-trnC-UGC TGTTCCCTCTTTTTCATCCCC CCGGATTTGAACTGGGGAAA 1175–1178 1.000 70.6
rpoB-trnC-UGC_p4 rpoB-trnC-UGC CCGGGTATTGTAGATGTTCCC AAGTCTGTTATTGAGGCGGC 1211–1214 1.000 69.5
rpoB-trnC-UGC_p5 rpoB-trnC-UGC CCTCTTTTTCATCCCCAAGC CCGGATTTGAACTGGGGAAA 1170–1173 1.000 69.3

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
Murbeckiella boryi NC_049667.1 154730 View on NCBI ↗
Murbeckiella pinnatifida NC_049677.1 154922 View on NCBI ↗