Markers + reference

Forsythia

7 species · Oleaceae · Lamiales

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Species 7
Genome length 156–156 kb
Candidate markers 265
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 9 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 451 0.0074 1.00 56.1 yes View details
matK-rps16 LSC 1606 0.0049 0.99 54.5 yes View details
rps2 LSC 711 0.0012 1.00 29.9 yes View details
psbZ-trnG(GCC) LSC 298 0.0000 1.00 34.9 yes View details
trnG(GCC)-trnfM(CAU) LSC 169 0.0189 0.99 56.7 yes View details
accD-psaI LSC 701 0.0045 1.00 41.5 yes View details
rpl16 LSC 1272 0.0032 1.00 39.5 yes View details
ycf1 IRb 1164 0.0015 1.00 47.3 no View details
ndhF SSC 2217 0.0025 1.00 47.5 yes View details
ndhF-rpl32 SSC 511 0.0114 1.00 60.7 yes View details
ndhA SSC 2193 0.0034 1.00 54.5 yes View details
rps15 SSC 273 0.0021 1.00 26.6 yes View details
ycf1 SSC 5616 0.0033 0.99 40.5 yes View details
rps16-trnQ(UUG) LSC 1742 0.0027 0.99 57.2 yes View details
trnC(GCA)-petN LSC 828 0.0031 0.99 56.8 yes View details
trnM(CAU)-psbD LSC 1326 0.0009 1.00 54.4 yes View details
psbM-trnD(GUC) LSC 1072 0.0019 1.00 52.0 yes View details
trnE(UUC)-trnM(CAU) LSC 808 0.0019 0.97 51.8 yes View details
petA-psbJ LSC 928 0.0030 1.00 50.4 yes View details
petB LSC 1353 0.0027 1.00 50.4 yes View details
psaB LSC 2205 0.0009 1.00 49.9 yes View details
atpF LSC 1261 0.0021 1.00 49.7 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 105 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 TTCCCTCTAGACCTAGCTGC 582–592 1.000 79.9
trnH(GUG)-psbA_p2 trnH(GUG)-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 528–538 1.000 79.5
trnH(GUG)-psbA_p3 trnH(GUG)-psbA CCTTAATCCACTTGGCCACA TTCCCTCTAGACCTAGCTGC 524–534 1.000 79.1
trnH(GUG)-psbA_p4 trnH(GUG)-psbA TTAGTTATGGGCGAACGACG CCGTGCTAACCTTGGTATGG 631–641 1.000 77.7
trnH(GUG)-psbA_p5 trnH(GUG)-psbA TTAGTTATGGGCGAACGACG ACCGTGCTAACCTTGGTATG 632–642 1.000 77.3
matK-rps16_p1 matK-rps16 CCTGATCATGAGCAAGTGCA GGTGCTCAACCTACAGGAAC 1779–1802 1.000 78.9
matK-rps16_p2 matK-rps16 ACCCTGATCATGAGCAAGTG GGTGCTCAACCTACAGGAAC 1781–1804 1.000 77.6
matK-rps16_p3 matK-rps16 CCTGATCATGAGCAAGTGCA GTGCTCAACCTACAGGAACT 1778–1801 1.000 73.7
matK-rps16_p4 matK-rps16 CCCTGATCATGAGCAAGTGC GGTGCTCAACCTACAGGAAC 1780–1803 1.000 73.1
matK-rps16_p5 matK-rps16 ACCCTGATCATGAGCAAGTG GTGCTCAACCTACAGGAACT 1780–1803 1.000 72.4
rps16-trnQ(UUG)_p1 rps16-trnQ(UUG) CGGATCTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1795–1829 1.000 81.0
rps16-trnQ(UUG)_p2 rps16-trnQ(UUG) ATCTGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1792–1826 1.000 81.0
rps16-trnQ(UUG)_p3 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1781–1815 1.000 80.6
rps16-trnQ(UUG)_p4 rps16-trnQ(UUG) CCACAACGGATCTGTCCTTC GAGGTTCGAATCCTTCCGTC 1801–1835 1.000 79.5
rps16-trnQ(UUG)_p5 rps16-trnQ(UUG) GGATCTGTCCTTCAAGTCGC GAGGTTCGAATCCTTCCGTC 1794–1828 1.000 78.8
atpF_p1 atpF GGCTCGAATGGTTACCATGA AGGCAAAGTGATACAAAAAGAACT 1391–1393 1.000 40.5
atpF_p2 atpF GGCTCGAATGGTTACCATGA ACTCTGATCGATTTTTGAGTCT 1370–1372 1.000 40.5
atpF_p3 atpF GGCTCGAATGGTTACCATGA AGAACTCTGATCGATTTTTGAGTC 1373–1375 1.000 40.5
atpF_p4 atpF GGCTCGAATGGTTACCATGA GAACTCTGATCGATTTTTGAGTCT 1372–1374 1.000 40.5
atpF_p5 atpF GGCTCGAATGGTTACCATGA GGCAAAGTGATACAAAAAGAACTC 1390–1392 1.000 40.5
rps2_p1 rps2 ACGTGAGTAAAGCCAAAGCA GGTCGGATCGATTGGTTGAA 1838–1842 1.000 80.3
rps2_p2 rps2 GGAAACCCCCTATTTGCCAA GGTCGGATCGATTGGTTGAA 1505–1509 1.000 80.3
rps2_p3 rps2 ACGTGAGTAAAGCCAAAGCA ACCCCTTGGTACCGGATTTA 1782–1786 1.000 80.2
rps2_p4 rps2 ACGTGAGTAAAGCCAAAGCA TACCCCTTGGTACCGGATTT 1783–1787 1.000 80.2
rps2_p5 rps2 ACGTGAGTAAAGCCAAAGCA TTGGATTATTGCGAGCGGAA 2002–2006 1.000 80.1
trnC(GCA)-petN_p1 trnC(GCA)-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 931–938 1.000 80.6
trnC(GCA)-petN_p2 trnC(GCA)-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 929–936 1.000 80.6
trnC(GCA)-petN_p3 trnC(GCA)-petN GTATCATTTTGGCGGCATGG ACTTCTTCCCCACACTACGA 983–990 1.000 80.1
trnC(GCA)-petN_p4 trnC(GCA)-petN GTATCATTTTGGCGGCATGG TTCTTCCCCACACTACGAGT 981–988 1.000 80.1
trnC(GCA)-petN_p5 trnC(GCA)-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 932–939 1.000 80.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Forsythia giraldiana NC_056245.1 156383 View on NCBI ↗
Forsythia mandschurica NC_048504.1 156396 View on NCBI ↗
Forsythia mira NC_046065.1 156485 View on NCBI ↗
Forsythia saxatilis NC_051493.1 156376 View on NCBI ↗
Forsythia suspensa NC_036367.1 156404 View on NCBI ↗
Forsythia viridissima MW856917.1 156473 View on NCBI ↗
Forsythia x intermedia NC_036982.1 156376 View on NCBI ↗