Markers + reference

Matthiola

5 species · Brassicaceae · Brassicales

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Species 5
Genome length 152–154 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 297 0.1097 0.89 72.8 yes View details
trnK-UUU-rps16 LSC 587 0.0670 1.00 84.5 yes View details
trnS-GCU-trnG-GGA LSC 657 0.0600 0.94 84.7 yes View details
trnT-UGU-trnL-UAA LSC 832 0.0449 0.98 83.9 yes View details
petA-psbJ LSC 1041 0.0668 0.94 80.8 yes View details
trnP-UGG-psaJ LSC 380 0.0578 1.00 81.8 yes View details
ycf1 IRb 1032 0.0083 1.00 52.1 no View details
ndhF-rpl32 SSC 883 0.0621 0.97 83.4 yes View details
rpl32-trnL-UAG SSC 551 0.0736 1.00 82.4 yes View details
ndhG-ndhI SSC 395 0.1065 0.91 76.9 yes View details
ycf1 SSC 5373 0.0409 1.00 67.4 yes View details
trnE-UUC-trnT-GGU LSC 718 0.0527 1.00 87.3 yes View details
rbcL-accD LSC 719 0.0498 0.98 83.9 yes View details
petN-psbM LSC 530 0.0492 1.00 82.6 yes View details
trnG-GGA-trnR-UCU LSC 168 0.0879 0.98 82.2 yes View details
psbK-psbI LSC 499 0.0554 0.84 81.9 yes View details
trnF-GAA-ndhJ LSC 531 0.0431 0.96 81.5 yes View details
accD-psaI LSC 731 0.0504 0.93 81.1 yes View details
psaJ-rpl33 LSC 424 0.0536 0.99 81.0 yes View details
psbM-trnD-GUC LSC 938 0.0456 0.99 80.7 yes View details
ccsA-ndhD SSC 211 0.0572 0.96 80.7 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-GUG-psbA_p1 trnH-GUG-psbA CCACTGCCTTATCCACTTGG ATATTCAGCTCCCGTTGCAG 952 0.200 45.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CCACTGCCTTATCCACTTGG TGTTGAGGCTCCATCTACCA 355 0.200 45.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CCACTGCCTTATCCACTTGG GCTGTTGAGGCTCCATCTAC 357 0.200 45.6
trnH-GUG-psbA_p4 trnH-GUG-psbA CCACTGCCTTATCCACTTGG ATGCACCCATTCCACATGTT 810 0.200 45.6
trnH-GUG-psbA_p5 trnH-GUG-psbA CCACTGCCTTATCCACTTGG GGTGTAGCTGGTGTATTCGG 789 0.200 45.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CATGCGTGAATCAAGCGTTT 1444–1512 1.000 88.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 949–980 0.800 79.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TGCGATACGGTCAAAGTGAG CATGCGTGAATCAAGCGTTT 2030 0.200 47.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 TGCGATACGGTCAAAGTGAG CCCAATGAGCCGTTTATCGA 1535 0.200 47.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TGCGATACGGTCAAAGTGAG TCCCAATGAGCCGTTTATCG 1536 0.200 47.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACGTCCTGGATCATTAGATAGGA 519–619 1.000 65.7
psbK-psbI_p2 psbK-psbI TGGCAAGCAGCTGTAAGTTT ACGTCCTGGATCATTAGATAGGA 516–616 1.000 63.8
psbK-psbI_p3 psbK-psbI TTGGCAAGCAGCTGTAAGTT ACGTCCTGGATCATTAGATAGGA 517–617 1.000 63.7
psbK-psbI_p4 psbK-psbI TTTGGCAAGCAGCTGTAAGT ACGTCCTGGATCATTAGATAGGA 518–618 1.000 63.7
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG GGATTACGTCCTGGATCATT 524–624 1.000 62.6
trnS-GCU-trnG-GGA_p1 trnS-GCU-trnG-GGA CCAACGCTTTAGTCCACTCA ACGAATCACACTTTTACCACT 719–819 1.000 62.2
trnS-GCU-trnG-GGA_p2 trnS-GCU-trnG-GGA AACGCTTTAGTCCACTCAGC ACGAATCACACTTTTACCACT 717–817 1.000 61.9
trnS-GCU-trnG-GGA_p3 trnS-GCU-trnG-GGA CCAACGCTTTAGTCCACTCA AACGAATCACACTTTTACCACT 720–820 1.000 60.3
trnS-GCU-trnG-GGA_p4 trnS-GCU-trnG-GGA GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 714–814 1.000 60.3
trnS-GCU-trnG-GGA_p5 trnS-GCU-trnG-GGA AACGCTTTAGTCCACTCAGC AACGAATCACACTTTTACCACT 718–818 1.000 60.0
trnG-GGA-trnR-UCU_p1 trnG-GGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTATGTCCT 248–265 1.000 55.7
trnG-GGA-trnR-UCU_p2 trnG-GGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTATGTCCTATCCA 242–259 1.000 55.7
trnG-GGA-trnR-UCU_p3 trnG-GGA-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGGTTTAGAAGACCTATGTCCT 254–271 1.000 55.5
trnG-GGA-trnR-UCU_p4 trnG-GGA-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGAAGACCTATGTCCTATCCA 248–265 1.000 55.5
trnG-GGA-trnR-UCU_p5 trnG-GGA-trnR-UCU AAACCCTTAGCCTTCCAAGC AGGTTTAGAAGACCTATGTCCT 256–273 1.000 55.0
petN-psbM_p1 petN-psbM TCGTAGTGTGGGGAAGAAGT AGTTCGAATCCAACCAAGGA 1249–1312 0.600 62.4
petN-psbM_p2 petN-psbM CGTAGTGTGGGGAAGAAGTG AGTTCGAATCCAACCAAGGA 1248–1311 0.600 61.8
petN-psbM_p3 petN-psbM CTCTCGTAGTGTGGGGAAGA AGTTCGAATCCAACCAAGGA 1252–1315 0.600 61.1
petN-psbM_p4 petN-psbM CTCTCTCGTAGTGTGGGGAA AGTTCGAATCCAACCAAGGA 1254–1317 0.600 61.1
petN-psbM_p5 petN-psbM TCTCTCGTAGTGTGGGGAAG AGTTCGAATCCAACCAAGGA 1253–1316 0.600 61.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Matthiola fruticulosa subsp. valesiaca PP165059.1 154076 View on NCBI ↗
Matthiola incana NC_034358.1 153896 View on NCBI ↗
Matthiola longipetala NC_049670.1 153860 View on NCBI ↗
Matthiola ovatifolia NC_049674.1 152104 View on NCBI ↗
Matthiola stoddartii NC_081130.1 153354 View on NCBI ↗