Markers + reference

Scrophularia

32 species · Scrophulariaceae · Lamiales

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Species 32
Genome length 152–154 kb
Candidate markers 273
Primer pairs 105

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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 306 0.0693 0.94 75.4 yes View details
trnS-GCU-trnG-UCC LSC 729 0.0152 1.00 70.1 yes View details
psaA-ycf3 LSC 738 0.0147 0.99 65.6 yes View details
trnT-UGU-trnL-UAA LSC 713 0.0117 0.97 73.6 yes View details
ndhC-trnV-UAC LSC 1098 0.0161 1.00 68.3 yes View details
petA-psbJ LSC 1040 0.0144 0.99 68.6 yes View details
ycf1 IRb 226 0.0113 1.00 41.9 no View details
ndhF SSC 2232 0.0099 1.00 57.0 yes View details
rpl32-trnL-UAG SSC 866 0.0223 1.00 70.3 yes View details
ndhA SSC 2141 0.0080 1.00 56.5 yes View details
rps15-ycf1 SSC 395 0.0112 1.00 54.2 yes View details
ycf1 SSC 4698 0.0109 1.00 54.5 yes View details
trnK-UUU-rps16 LSC 485 0.0157 0.99 80.3 yes View details
trnT-GGU-psbD LSC 1332 0.0122 1.00 74.8 yes View details
ycf3-trnS-GGA LSC 648 0.0118 1.00 70.6 yes View details
rps4-trnT-UGU LSC 386 0.0198 1.00 69.6 yes View details
rpoB-trnC-GCA LSC 1120 0.0117 1.00 69.3 yes View details
psbK-psbI LSC 372 0.0152 0.99 67.9 yes View details
ndhD-psaC SSC 119 0.0423 0.99 67.7 yes View details
petN-psbM LSC 933 0.0113 1.00 67.4 yes View details
trnC-GCA-petN LSC 851 0.0114 1.00 67.3 yes View details
atpH-atpI LSC 1024 0.0101 0.99 67.0 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 GATCCACTTGGCTACATCCG GAGTGGGAGCTTAGTTTCCG 999–1196 1.000 90.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGCTTAGTTTCCGTCTGGG 993–1190 0.969 89.0
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGAGCTTAGTTTCCGTCTGG 994–1191 0.969 89.0
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGGAGCTTAGTTTCCGTCTG 995–1192 0.969 89.0
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGCTTAGTTTCCGTCTGGG 1007–1204 0.969 88.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCCACAGGAAC 459–614 1.000 76.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGGAAC 458–613 1.000 76.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GTGCTCAACCCACAGGAAC 473–628 1.000 75.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC GTGCTCAACCCACAGGAAC 544–699 1.000 75.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT GTGCTCAACCCACAGGAAC 543–698 1.000 75.5
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT GGATTACGTCCCGGATCATT 435–502 1.000 84.3
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGTCCGGGATTAC 443–510 0.969 84.3
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT TTCTTCACGTCCGGGATTAC 448–515 0.969 84.2
psbK-psbI_p4 psbK-psbI TATGCCAGTCATCCCTCTGT TTCTTCACGTCCGGGATTAC 483–550 0.969 82.8
psbK-psbI_p5 psbK-psbI GCCAGTCATCCCTCTGTTTT TTCTTCACGTCCGGGATTAC 480–547 0.969 82.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 785–841 1.000 62.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 784–840 1.000 62.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 788–844 1.000 61.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 787–843 1.000 61.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 786–842 1.000 61.7
atpH-atpI_p1 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1128–1188 0.969 84.5
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TCCCTGTCATGTTCCTTGGA 1113–1164 0.938 84.4
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TCCCTGTCATGTTCCTTGGA 1114–1165 0.938 83.2
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 1123–1183 0.938 82.7
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1065–1116 0.875 79.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CATTGCCTCATTTGCATCCC CCGGATTTGAACTGGGGAAA 978–1221 1.000 87.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CATTGCCTCATTTGCATCCC AAAAGGATTTGCAGTCCCCC 960–1203 1.000 85.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTGCCTCATTTGCATCCCC CCGGATTTGAACTGGGGAAA 977–1220 1.000 82.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CATTGCCTCATTTGCATCCC TTTGTTGATCAGGCGACACC 997–1240 1.000 82.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ACATTGCCTCATTTGCATCC CCGGATTTGAACTGGGGAAA 979–1222 1.000 81.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (32)

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

Species Accession Length (bp) Link
Scrophularia alaschanica OR393409.1 151997 View on NCBI ↗
Scrophularia amgunensis OR393399.1 153173 View on NCBI ↗
Scrophularia buergeriana NC_031437.1 153631 View on NCBI ↗
Scrophularia canina PP622689.1 152723 View on NCBI ↗
Scrophularia cephalantha NC_057296.1 153016 View on NCBI ↗
Scrophularia chasmophila OR393407.1 152335 View on NCBI ↗
Scrophularia delavayi OR393414.1 153050 View on NCBI ↗
Scrophularia dentata NC_036942.1 152600 View on NCBI ↗
Scrophularia elatior OR393401.1 153239 View on NCBI ↗
Scrophularia fargesii OR393413.1 152429 View on NCBI ↗
Scrophularia henryi NC_036943.1 152868 View on NCBI ↗
Scrophularia heucheriiflora OR393400.1 152536 View on NCBI ↗
Scrophularia hypsophila OR393420.1 152080 View on NCBI ↗
Scrophularia incisa NC_081995.1 152481 View on NCBI ↗
Scrophularia integrifolia NC_081997.1 152088 View on NCBI ↗
Scrophularia jinii OR393405.1 152313 View on NCBI ↗
Scrophularia kiriloviana NC_081996.1 152554 View on NCBI ↗
Scrophularia lijangensis OR393402.1 152668 View on NCBI ↗
Scrophularia mandarinorum OR393419.1 152879 View on NCBI ↗
Scrophularia mapienensis OR393411.1 153153 View on NCBI ↗
Scrophularia marilandica PQ679323.1 152414 View on NCBI ↗
Scrophularia modesta OR393403.1 152997 View on NCBI ↗
Scrophularia musashiensis OR393404.1 152401 View on NCBI ↗
Scrophularia ningpoensis NC_053823.1 153175 View on NCBI ↗
Scrophularia nodosa PP622690.1 152414 View on NCBI ↗
Scrophularia spicata OR393415.1 152887 View on NCBI ↗
Scrophularia stylosa OR393416.1 152944 View on NCBI ↗
Scrophularia taihangshanensis OR393412.1 153221 View on NCBI ↗
Scrophularia takesimensis NC_026202.1 152425 View on NCBI ↗
Scrophularia wattii OR393408.1 152495 View on NCBI ↗
Scrophularia yoshimurae NC_087760.1 153173 View on NCBI ↗
Scrophularia yunnanensis OR393410.1 152711 View on NCBI ↗