Markers + reference

Hedera

4 species · Araliaceae · Apiales

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Species 4
Genome length 157–157 kb
Candidate markers 264
Primer pairs 105

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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 898 0.0022 1.00 51.1 yes View details
rps16 LSC 1127 0.0006 1.00 27.0 yes View details
rpoC1 LSC 2830 0.0006 1.00 44.4 yes View details
psbM-trnD-GUC LSC 1172 0.0016 1.00 49.0 yes View details
ycf3-trnS-GGA LSC 863 0.0017 1.00 45.9 yes View details
trnT-UGU-trnL-UAA LSC 823 0.0020 1.00 50.7 yes View details
accD-psaI LSC 699 0.0021 1.00 50.9 yes View details
trnP-UGG-psaJ LSC 386 0.0030 1.00 38.4 yes View details
ycf15-trnL-CAA IRb 320 0.0063 1.00 43.2 yes View details
ycf1 IRb 1506 0.0000 1.00 40.0 no View details
ndhF-rpl32 SSC 1179 0.0013 1.00 50.3 yes View details
ycf1 SSC 5631 0.0005 1.00 52.9 yes View details
ndhB-trnL-CAA IRa 578 0.0000 1.00 35.2 yes View details
trnT-GGU-psbD LSC 1377 0.0012 1.00 60.2 yes View details
rps16-trnQ-UUG LSC 1766 0.0012 1.00 59.1 yes View details
petN-psbM LSC 880 0.0013 0.98 51.9 yes View details
rpl32-trnL-UAG SSC 813 0.0014 0.99 51.0 yes View details
petA-psbJ LSC 1034 0.0011 1.00 50.1 yes View details
ndhC-trnM-CAU LSC 1850 0.0005 1.00 49.4 yes View details
ndhA SSC 2161 0.0010 1.00 48.7 yes View details
trnS-CGA-trnR-UCU LSC 225 0.0025 0.90 47.5 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGTCCGTGTCAACCAATATCT AGTTCAATGATTTGATTGTCTTGTCT 2794–2809 1.000 40.1
trnK-UUU_p2 trnK-UUU TGTCCGTGTCAACCAATATCT AGTTCAATGATTTGATTGTCTTGTC 2794–2809 1.000 40.1
trnK-UUU_p3 trnK-UUU TGTCCGTGTCAACCAATATCT GTTCAATGATTTGATTGTCTTGTCT 2793–2808 1.000 40.1
trnK-UUU_p4 trnK-UUU TGTCCGTGTCAACCAATATCT TCAATGATTTGATTGTCTTGTCT 2791–2806 1.000 40.1
trnK-UUU_p5 trnK-UUU TGTCCGTGTCAACCAATATCT AGTTCAATGATTTGATTGTCTTGT 2794–2809 1.000 40.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCTTCGCTTCATCCA TTCCTTGAAAAAGGCGCTCA 1050–1084 1.000 77.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1063–1097 1.000 77.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 1002–1036 1.000 76.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 1001–1035 1.000 76.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1087–1121 1.000 76.1
rps16_p1 rps16 TTCGTTTGATTAGGGCAAAG TGTACCGACTGAACCAATGAC 1231–1232 1.000 41.4
rps16_p2 rps16 TTTCGTTTGATTAGGGCAAAG TGTACCGACTGAACCAATGAC 1232–1233 1.000 40.1
rps16_p3 rps16 TTCGTTTGATTAGGGCAAAG GTACCGACTGAACCAATGACT 1230–1231 1.000 40.1
rps16_p4 rps16 TTTCGTTTGATTAGGGCAAAG GTACCGACTGAACCAATGACT 1231–1232 1.000 40.1
rps16_p5 rps16 TTCGTTTGATTAGGGCAAAG TGTACCGACTGAACCAATGA 1231–1232 1.000 40.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1838–1845 1.000 78.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1853–1860 1.000 76.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1852–1859 1.000 76.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1842–1849 1.000 73.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1868–1875 1.000 73.7
trnS-CGA-trnR-UCU_p1 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 284–306 1.000 67.6
trnS-CGA-trnR-UCU_p2 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 287–309 1.000 67.4
trnS-CGA-trnR-UCU_p3 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 290–312 1.000 67.0
trnS-CGA-trnR-UCU_p4 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 293–315 1.000 66.7
trnS-CGA-trnR-UCU_p5 trnS-CGA-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 288–310 1.000 65.2
rpoC1_p1 rpoC1 ACTTAGCTTAGGTACCATCTGA TTGCTCGTTCGAGAACTACG 2948–2954 1.000 45.7
rpoC1_p2 rpoC1 ACTTAGCTTAGGTACCATCTGA ACGATCTTTGGCTCTGGAAC 2931–2937 1.000 45.2
rpoC1_p3 rpoC1 ACTTAGCTTAGGTACCATCTGA TTCGATTGCTCGTTCGAGAA 2953–2959 1.000 43.3
rpoC1_p4 rpoC1 ACTTAGCTTAGGTACCATCTGA TTTCGATTGCTCGTTCGAGA 2954–2960 1.000 43.3
rpoC1_p5 rpoC1 ACTTAGCTTAGGTACCATCTGA CGATTGCTCGTTCGAGAACT 2951–2957 1.000 43.0

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
Hedera helix NC_070394.1 156602 View on NCBI ↗
Hedera helix subsp. helix OR896879.1 156691 View on NCBI ↗
Hedera nepalensis var. sinensis MK130890.1 156652 View on NCBI ↗
Hedera rhombea MT991757.1 156680 View on NCBI ↗