Markers + reference

Smelowskia

4 species · Brassicaceae · Brassicales

Back to catalogue

Species 4
Genome length 154–155 kb
Candidate markers 270
Primer pairs 100

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 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-AGC-trnG-GGA LSC 611 0.0512 0.93 87.3 yes View details
rpoB-trnC-UGC LSC 1113 0.0308 1.00 67.8 yes View details
psbM-trnD-GAC LSC 1049 0.0361 0.94 72.1 yes View details
trnE-GAA-trnT-ACC LSC 816 0.0329 0.98 76.6 yes View details
trnT-ACA-trnL-UUA LSC 674 0.0390 0.96 75.1 yes View details
trnL-UUA-trnF-UUC LSC 512 0.0612 0.95 80.7 yes View details
trnF-UUC-ndhJ LSC 583 0.0274 1.00 69.1 yes View details
petA-psbJ LSC 980 0.0398 0.99 76.5 yes View details
trnP-CCA-psaJ LSC 369 0.0244 1.00 61.1 yes View details
ycf1 IRb 1041 0.0024 1.00 37.4 no View details
ndhF-rpl32 SSC 888 0.0631 0.96 85.1 yes View details
rpl32-trnL-CUA SSC 540 0.0602 0.98 81.9 yes View details
ycf1 SSC 5370 0.0250 1.00 55.8 yes View details
rps16-trnQ-CAA LSC 458 0.0393 0.99 83.4 yes View details
trnW-UGG-trnP-CCA LSC 188 0.0567 0.99 81.8 yes View details
psbZ-trnG-GGC LSC 476 0.0361 1.00 80.6 yes View details
trnK-AAA-rps16 LSC 578 0.0421 1.00 80.1 yes View details
trnH-CAC-psbA LSC 221 0.0538 0.99 79.0 yes View details
ndhE-ndhG SSC 254 0.0489 0.99 78.5 yes View details
psaJ-rpl33 LSC 442 0.0434 0.99 78.1 yes View details
trnD-GAC-trnY-UAC LSC 432 0.0432 1.00 77.9 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 100 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 CCTCTAGACCTAGCTGCTGT 294–373 1.000 87.2
trnH-CAC-psbA_p2 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 297–376 1.000 87.0
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TGTTAGGTGTAGCCGGTGTA 716–795 1.000 82.5
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 279–358 0.750 73.8
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 280–359 0.750 73.6
trnK-AAA-rps16_p1 trnK-AAA-rps16 TACCGTTGAGTTAGCAACCC ACGGAATTAAGTCTTAATAAAACGA 634–764 0.750 37.4
trnK-AAA-rps16_p2 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT ACGGAATTAAGTCTTAATAAAACGA 648–778 0.750 37.3
trnK-AAA-rps16_p3 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT ACGGAATTAAGTCTTAATAAAACGA 647–777 0.750 37.3
trnK-AAA-rps16_p4 trnK-AAA-rps16 AACTCTACCGCAGATCTGGA ACGGAATTAAGTCTTAATAAAACGA 716–846 0.750 37.1
trnK-AAA-rps16_p5 trnK-AAA-rps16 AACTCTACCGCAGATCTGGA ACGGAATTAAGTCTTAATAAAACGAA 716–846 0.750 37.1
rps16-trnQ-CAA_p1 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 515–531 1.000 87.5
rps16-trnQ-CAA_p2 rps16-trnQ-CAA CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 525–541 1.000 86.6
rps16-trnQ-CAA_p3 rps16-trnQ-CAA CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 541–557 1.000 85.0
rps16-trnQ-CAA_p4 rps16-trnQ-CAA TCCACAGCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 542–558 1.000 84.9
rps16-trnQ-CAA_p5 rps16-trnQ-CAA ATCCACAGCAGATCATGTCC GAGGTTCGAATCCTTCCGTC 543–559 1.000 83.2
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTT 670–761 1.000 76.6
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA ATCAAACCGAGAGACCCTTT 669–760 1.000 76.6
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC AATCAAACCGAGAGACCCTT 668–759 1.000 76.3
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC ATCAAACCGAGAGACCCTTT 667–758 1.000 76.3
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTTT 670–761 1.000 74.7
rpoB-trnC-UGC_p1 rpoB-trnC-UGC CACGAGCCCATATTCTTGCT CCGGATTTGAACTGGGGAAA 1680–1689 1.000 83.7
rpoB-trnC-UGC_p2 rpoB-trnC-UGC ATTGGATCCCCACCTACACA CCGGATTTGAACTGGGGAAA 1879–1888 1.000 83.4
rpoB-trnC-UGC_p3 rpoB-trnC-UGC ATTGGATCCCCACCTACACA ACCACAAGCAAATGGACACT 2352 0.500 59.8
rpoB-trnC-UGC_p4 rpoB-trnC-UGC CACGAGCCCATATTCTTGCT ACCACAAGCAAATGGACACT 2153 0.500 59.7
rpoB-trnC-UGC_p5 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC ACCACAAGCAAATGGACACT 1665 0.500 59.0
psbM-trnD-GAC_p1 psbM-trnD-GAC TCGTAGTGTGGGGAAGAAGT CGATCTTGCTAAGGATCCCG 2039–2083 1.000 87.9
psbM-trnD-GAC_p2 psbM-trnD-GAC CGTAGTGTGGGGAAGAAGTG CGATCTTGCTAAGGATCCCG 2038–2082 1.000 87.3
psbM-trnD-GAC_p3 psbM-trnD-GAC TCGTAGTGTGGGGAAGAAGT AAGTATGCCCCCATCGTCTA 2407–2451 1.000 87.0
psbM-trnD-GAC_p4 psbM-trnD-GAC CTCTCGTAGTGTGGGGAAGA CGATCTTGCTAAGGATCCCG 2042–2086 1.000 86.6
psbM-trnD-GAC_p5 psbM-trnD-GAC CGTAGTGTGGGGAAGAAGTG AAGTATGCCCCCATCGTCTA 2406–2450 1.000 86.4

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
Smelowskia altaica MK637789.1 154670 View on NCBI ↗
Smelowskia annua MK637791.1 153549 View on NCBI ↗
Smelowskia calycina MK637794.1 154901 View on NCBI ↗
Smelowskia flavissima MK637798.1 154947 View on NCBI ↗