Markers + reference

Chengiodendron

2 species · Oleaceae · Lamiales

Back to catalogue

Species 2
Genome length 156–156 kb
Candidate markers 266
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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH(GUG)-psbA LSC 434 0.0023 1.00 56.6 yes View details
matK LSC 1521 0.0007 1.00 59.1 yes View details
rps16 LSC 1144 0.0009 1.00 59.3 yes View details
rps16-trnQ(UUG) LSC 1582 0.0006 1.00 58.9 yes View details
petA-psbJ LSC 952 0.0021 1.00 60.0 yes View details
clpP LSC 2048 0.0005 1.00 57.9 yes View details
ycf1 IRb 1164 0.0000 1.00 40.0 no View details
ndhF-rpl32 SSC 478 0.0042 1.00 58.6 yes View details
rpl32-trnL(UAG) SSC 839 0.0024 1.00 60.1 yes View details
ndhD SSC 1503 0.0007 1.00 59.1 yes View details
ycf1 SSC 5631 0.0005 1.00 52.8 yes View details
trnS(GCU)-trnG(GCC) LSC 706 0.0014 1.00 59.6 yes View details
rbcL-accD LSC 669 0.0015 1.00 59.6 yes View details
trnC(GCA)-petN LSC 774 0.0013 1.00 59.5 yes View details
psbD LSC 1062 0.0009 1.00 59.3 yes View details
ccsA SSC 972 0.0010 1.00 59.3 yes View details
atpF LSC 1252 0.0008 1.00 59.2 yes View details
petB LSC 1354 0.0007 1.00 59.2 yes View details
petD LSC 1215 0.0008 1.00 59.2 yes View details
ycf3-trnS(GGA) LSC 796 0.0000 1.00 58.9 yes View details
ycf3 LSC 1964 0.0000 1.00 57.8 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 614 1.000 76.7
trnH(GUG)-psbA_p2 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 559 1.000 76.4
trnH(GUG)-psbA_p3 trnH(GUG)-psbA TTAGTTATGGGCGAACGACG ACCGTGCTAACCTTGGTATG 615 1.000 76.3
trnH(GUG)-psbA_p4 trnH(GUG)-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 560 1.000 76.2
trnH(GUG)-psbA_p5 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 560 1.000 75.9
matK_p1 matK ACATCAACATTTCAGAATAGTGGA AGTTTACCTGTTTCCGAGGT 1739 1.000 40.0
matK_p2 matK ACATCAACATTTCAGAATAGTGGA AAGTTTACCTGTTTCCGAGGT 1740 1.000 40.0
matK_p3 matK ACATCAACATTTCAGAATAGTGGAA AGTTTACCTGTTTCCGAGGT 1739 1.000 40.0
matK_p4 matK ACATCAACATTTCAGAATAGTGG AGTTTACCTGTTTCCGAGGT 1739 1.000 40.0
matK_p5 matK ACATCAACATTTCAGAATAGTGGA CCTTGTTTTGACTGTATCGCA 1700 1.000 40.0
rps16_p1 rps16 TCGACAGAAGCAATGAGAAA TCAATTCCATACCGGTTCCA 1298 1.000 44.5
rps16_p2 rps16 TTCGACAGAAGCAATGAGAA TCAATTCCATACCGGTTCCA 1299 1.000 44.5
rps16_p3 rps16 CGAATAAAGCAGGATTAAGGGG TCAATTCCATACCGGTTCCA 1272 1.000 43.4
rps16_p4 rps16 TTCGACAGAAGCAATGAGAAA TCAATTCCATACCGGTTCCA 1299 1.000 42.9
rps16_p5 rps16 TCGACAGAAGCAATGAGAAA TCAATTCCATACCGGTTCCAA 1298 1.000 42.5
rps16-trnQ(UUG)_p1 rps16-trnQ(UUG) CGGATCTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1669 1.000 78.8
rps16-trnQ(UUG)_p2 rps16-trnQ(UUG) ATCTGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1666 1.000 78.8
rps16-trnQ(UUG)_p3 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1655 1.000 78.3
rps16-trnQ(UUG)_p4 rps16-trnQ(UUG) CCACAACGGATCTGTCCTTC GAGGTTCGAATCCTTCCGTC 1675 1.000 77.3
rps16-trnQ(UUG)_p5 rps16-trnQ(UUG) GGATCTGTCCTTCAAGTCGC GAGGTTCGAATCCTTCCGTC 1668 1.000 76.6
trnS(GCU)-trnG(GCC)_p1 trnS(GCU)-trnG(GCC) CAATCCGACGCTTTAGTCCA AGACCGAAAGACCCTTTAACT 813 1.000 60.7
trnS(GCU)-trnG(GCC)_p2 trnS(GCU)-trnG(GCC) AATCCGACGCTTTAGTCCAC AGACCGAAAGACCCTTTAACT 812 1.000 60.7
trnS(GCU)-trnG(GCC)_p3 trnS(GCU)-trnG(GCC) ATCAACGGAACCGGAAAGAG AGACCGAAAGACCCTTTAACT 877 1.000 60.0
trnS(GCU)-trnG(GCC)_p4 trnS(GCU)-trnG(GCC) CATCAACGGAACCGGAAAGA AGACCGAAAGACCCTTTAACT 878 1.000 59.1
trnS(GCU)-trnG(GCC)_p5 trnS(GCU)-trnG(GCC) TCATCAACGGAACCGGAAAG AGACCGAAAGACCCTTTAACT 879 1.000 59.1
atpF_p1 atpF GGCTCGAATGGTTACCATGA AGGCAAAGTGATACAAAAAGAACT 1395 1.000 40.1
atpF_p2 atpF GGCTCGAATGGTTACCATGA ACTCTGATCGATTTTTGAGTCT 1374 1.000 40.1
atpF_p3 atpF GGCTCGAATGGTTACCATGA AGAACTCTGATCGATTTTTGAGTC 1377 1.000 40.1
atpF_p4 atpF GGCTCGAATGGTTACCATGA GAACTCTGATCGATTTTTGAGTCT 1376 1.000 40.1
atpF_p5 atpF GGCTCGAATGGTTACCATGA GGCAAAGTGATACAAAAAGAACTC 1394 1.000 40.1

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
Chengiodendron marginatum NC_042265.1 155562 View on NCBI ↗
Chengiodendron matsumuranum NC_072069.1 155560 View on NCBI ↗