Markers + reference

Noronhia

5 species · Oleaceae · Lamiales

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Species 5
Genome length 156–156 kb
Candidate markers 265
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH(GUG)-psbA LSC 444 0.0149 1.00 58.9 yes View details
psbK-psbI LSC 402 0.0095 1.00 59.6 yes View details
rps2 LSC 711 0.0006 1.00 29.3 yes View details
trnS(UGA)-psbZ LSC 352 0.0097 1.00 48.2 yes View details
ycf3-trnS(GGA) LSC 787 0.0095 1.00 51.8 yes View details
ndhC-trnM(CAU) LSC 1942 0.0050 1.00 61.7 yes View details
atpB-rbcL LSC 785 0.0107 1.00 45.8 yes View details
petA-psbJ LSC 951 0.0064 1.00 63.5 yes View details
psbE-petL LSC 1102 0.0064 1.00 56.8 yes View details
ycf1 IRb 1164 0.0021 1.00 50.6 no View details
rpl32-trnL(UAG) SSC 858 0.0058 1.00 59.5 yes View details
ycf1 SSC 5622 0.0050 1.00 46.2 yes View details
rps2-rpoC2 LSC 203 0.0286 1.00 73.2 yes View details
rpl2-trnH(GUG) LSC 83 0.0325 0.99 72.7 no View details
psbI-trnS(GCU) LSC 128 0.0312 0.98 72.0 yes View details
atpA-atpF LSC 64 0.0297 1.00 68.0 yes View details
rps19-rpl2 LSC 65 0.0231 1.00 66.9 yes View details
atpF-atpH LSC 362 0.0116 1.00 64.1 yes View details
psaA-ycf3 LSC 734 0.0041 1.00 62.9 yes View details
matK LSC 1521 0.0046 1.00 62.2 yes View details
ycf4-cemA LSC 868 0.0035 1.00 61.0 yes View details
petN-psbM LSC 1111 0.0018 1.00 60.2 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 TTAGTTATGGGCGAACGACG CCGTGCTAACCTTGGTATGG 623–628 1.000 78.8
trnH(GUG)-psbA_p2 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 568–573 1.000 78.6
trnH(GUG)-psbA_p3 trnH(GUG)-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 569–574 1.000 78.4
trnH(GUG)-psbA_p4 trnH(GUG)-psbA TTAGTTATGGGCGAACGACG ACCGTGCTAACCTTGGTATG 624–629 1.000 78.3
trnH(GUG)-psbA_p5 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 569–574 1.000 78.1
matK_p1 matK ACATCAACATTTCAGAATAGTGGA CCTTGTTTTGACTGTATCGCA 1700 1.000 41.5
matK_p2 matK ACATCAACATTTCAGAATAGTGGA AGTTTACCTGTTTCCGAGGT 1739 1.000 41.4
matK_p3 matK ACATCAACATTTCAGAATAGTGGA AAGTTTACCTGTTTCCGAGGT 1740 1.000 41.4
matK_p4 matK ACATCAACATTTCAGAATAGTGGAA AGTTTACCTGTTTCCGAGGT 1739 1.000 41.4
matK_p5 matK ACATCAACATTTCAGAATAGTGG AGTTTACCTGTTTCCGAGGT 1739 1.000 41.4
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 539–545 1.000 74.6
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 536–542 1.000 72.6
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 537–543 1.000 72.6
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 538–544 1.000 72.6
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGTCCAGGATTACG 540–546 1.000 72.2
psbI-trnS(GCU)_p1 psbI-trnS(GCU) CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 219–225 1.000 76.8
psbI-trnS(GCU)_p2 psbI-trnS(GCU) CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 220–226 1.000 76.8
psbI-trnS(GCU)_p3 psbI-trnS(GCU) CGTAATCCTGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 238–244 1.000 75.6
psbI-trnS(GCU)_p4 psbI-trnS(GCU) CGTAATCCTGGACGTGAAGAA TGGACTAAAGCGTCGGATTG 219–225 1.000 74.5
psbI-trnS(GCU)_p5 psbI-trnS(GCU) CGTAATCCTGGACGTGAAGAA GTGGACTAAAGCGTCGGATT 220–226 1.000 74.4
atpA-atpF_p1 atpA-atpF ACTAATTTCGTCGGCTCGAA TTGGGGGCGATGAAAGAAAT 123–134 1.000 76.7
atpA-atpF_p2 atpA-atpF AATTTCGTCGGCTCGAATGG TTGGGGGCGATGAAAGAAAT 120–131 1.000 74.0
atpA-atpF_p3 atpA-atpF ACTAATTTCGTCGGCTCGAA GTTGGGGGCGATGAAAGAAA 124–135 1.000 72.6
atpA-atpF_p4 atpA-atpF ACTAATTTCGTCGGCTCGAAT TTGGGGGCGATGAAAGAAAT 123–134 1.000 72.6
atpA-atpF_p5 atpA-atpF ACTAATTTCGTCGGCTCGAA AATATTGGCATGTTGGGGGC 135–146 1.000 71.3
atpF-atpH_p1 atpF-atpH TGGCCCAAAGAAACGAAAGA CCGAGGCAGAGGGAAAAATA 515–521 1.000 76.2
atpF-atpH_p2 atpF-atpH GTGGCCCAAAGAAACGAAAG CCGAGGCAGAGGGAAAAATA 516–522 1.000 75.6
atpF-atpH_p3 atpF-atpH AGTGGCCCAAAGAAACGAAA CCGAGGCAGAGGGAAAAATA 517–523 1.000 74.8
atpF-atpH_p4 atpF-atpH TTAAATCCGAAACTCCCGGC CCGAGGCAGAGGGAAAAATA 545–551 1.000 74.4
atpF-atpH_p5 atpF-atpH TGGCCCAAAGAAACGAAAGA GCAGAGGGAAAAATACGAGGT 510–516 1.000 73.8

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
Noronhia brevituba NC_042262.1 155594 View on NCBI ↗
Noronhia clarinerva NC_042275.1 155576 View on NCBI ↗
Noronhia intermedia NC_042276.1 155654 View on NCBI ↗
Noronhia lowryi NC_036984.1 155582 View on NCBI ↗
Noronhia peglerae NC_042426.1 155559 View on NCBI ↗