Markers + reference

Scolopia

2 species · Salicaceae · Malpighiales

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Species 2
Genome length 156–157 kb
Candidate markers 269
Primer pairs 105

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 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0028 1.00 60.4 yes View details
trnQ-UUG-psbK LSC 355 0.0056 1.00 42.9 yes View details
atpH-atpI LSC 1015 0.0039 1.00 47.5 yes View details
rpoB LSC 3213 0.0012 1.00 41.3 yes View details
petN-psbM LSC 1304 0.0023 0.98 61.6 yes View details
rbcL-accD LSC 742 0.0040 1.00 61.1 yes View details
petA-psbJ LSC 1162 0.0018 0.94 56.4 yes View details
clpP LSC 2054 0.0019 1.00 58.8 yes View details
psbB LSC 1527 0.0020 1.00 59.8 yes View details
rpl22 LSC 390 0.0026 1.00 42.6 yes View details
ndhF-trnL-UAG SSC 1923 0.0063 0.33 52.6 yes View details
rpoC1-rpoB LSC 26 0.0385 1.00 74.6 yes View details
rps19-trnH-GUG LSC 193 0.0000 0.99 70.9 no View details
rpl22-rps19 IRb 117 0.0427 1.00 66.4 yes View details
matK-trnK-UUU LSC 756 0.0053 1.00 61.8 yes View details
trnR-ACG-trnN-GUU IRb 635 0.0032 0.99 61.5 yes View details
trnN-GUU-trnR-ACG IRa 635 0.0032 0.99 61.5 yes View details
petB-petD LSC 979 0.0010 0.98 61.1 yes View details
accD-psaI LSC 660 0.0030 1.00 60.5 yes View details
ycf15-trnL-CAA IRb 755 0.0026 1.00 60.3 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
psbA_p1 psbA AGAAATTGGCGATTGCTCCT AGAATTCGTGTGCTTGGGAG 1173–1174 1.000 77.6
psbA_p2 psbA AGAAATTGGCGATTGCTCCT AGAGAATTCGTGTGCTTGGG 1175–1176 1.000 77.6
psbA_p3 psbA AGAAATTGGCGATTGCTCCT GAGAATTCGTGTGCTTGGGA 1174–1175 1.000 77.6
psbA_p4 psbA AGAAATTGGCGATTGCTCCT AATTCGTGTGCTTGGGAGTC 1171–1172 1.000 75.3
psbA_p5 psbA AGAAATTGGCGATTGCTCCT GAATTCGTGTGCTTGGGAGT 1172–1173 1.000 75.3
trnK-UUU_p1 trnK-UUU TGAATGAATTAAATTGAAGTGAGT TGTGTCGTACGATTCAATCTCT 2819 1.000 40.2
trnK-UUU_p2 trnK-UUU TGAATGAATTAAATTGAAGTGAGT TGTTTTGATTGTGTCGTACGA 2828 1.000 40.2
trnK-UUU_p3 trnK-UUU TGAATGAATTAAATTGAAGTGAGT TGTGTCGTACGATTCAATCTCTT 2819 1.000 40.2
trnK-UUU_p4 trnK-UUU TGAATGAATTAAATTGAAGTGAGT TTGTGTCGTACGATTCAATCTCT 2820 1.000 40.2
trnK-UUU_p5 trnK-UUU TGAATGAATTAAATTGAAGTGAGT TGATTGTGTCGTACGATTCA 2823 1.000 40.2
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCCGAAAGATAAGTGGG TGGGGTTGCTAACTCAATGG 880 1.000 67.7
matK-trnK-UUU_p2 matK-trnK-UUU CTCCCGAAAGATAAGTGGGT TGGGGTTGCTAACTCAATGG 879 1.000 67.7
matK-trnK-UUU_p3 matK-trnK-UUU ACTCCCGAAAGATAAGTGGG GGGGTTGCTAACTCAATGGT 879 1.000 67.6
matK-trnK-UUU_p4 matK-trnK-UUU CTCCCGAAAGATAAGTGGGT GGGGTTGCTAACTCAATGGT 878 1.000 67.6
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCCGAAAGATAAGTGGGT TGGGGTTGCTAACTCAATGG 880 1.000 67.0
trnQ-UUG-psbK_p1 trnQ-UUG-psbK CTTGGAGGTTCCCCTTCTCT CTTACAGCAGCTTGCCAAAC 1180 0.500 56.9
trnQ-UUG-psbK_p2 trnQ-UUG-psbK CTTGGAGGTTCCCCTTCTCT AGGATTACGCCCTGGATCAT 1702 0.500 55.2
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CTTGGAGGTTCCCCTTCTCT AAACTTACAGCAGCTTGCCA 1183 0.500 54.8
trnQ-UUG-psbK_p4 trnQ-UUG-psbK CTTGGAGGTTCCCCTTCTCT AACTTACAGCAGCTTGCCAA 1182 0.500 54.8
trnQ-UUG-psbK_p5 trnQ-UUG-psbK CTTGGAGGTTCCCCTTCTCT ACTTACAGCAGCTTGCCAAA 1181 0.500 54.8
atpH-atpI_p1 atpH-atpI CTCGCGATACCTTCTACAGC TATGGTCCATGGGTTCCCTT 1611 1.000 79.9
atpH-atpI_p2 atpH-atpI CTCGCGATACCTTCTACAGC GTGAATCCATGGAGGGACAC 1163 1.000 79.7
atpH-atpI_p3 atpH-atpI CCCGTTGGTTTATTGTCCCA TATGGTCCATGGGTTCCCTT 1885–1889 1.000 79.6
atpH-atpI_p4 atpH-atpI TCTCGTGTCCATTGCGAAAT TATGGTCCATGGGTTCCCTT 2019–2023 1.000 79.6
atpH-atpI_p5 atpH-atpI CTCGCGATACCTTCTACAGC ACCATTCCTACTGACGGTCA 1695 1.000 79.4
rpoC1-rpoB_p1 rpoC1-rpoB GTTGAGGCGAAACTGATCCA TTGCTCGTTCGAGAACTACG 174 1.000 78.6
rpoC1-rpoB_p2 rpoC1-rpoB TGTTGAGGCGAAACTGATCC TTGCTCGTTCGAGAACTACG 175 1.000 78.6
rpoC1-rpoB_p3 rpoC1-rpoB GTTGAGGCGAAACTGATCCA ACGATCTTTGGCTCTGGAAC 157 1.000 78.2
rpoC1-rpoB_p4 rpoC1-rpoB TGTTGAGGCGAAACTGATCC ACGATCTTTGGCTCTGGAAC 158 1.000 78.2
rpoC1-rpoB_p5 rpoC1-rpoB GTTGAGGCGAAACTGATCCA GGCTCTGGAACTGAAGCATT 148 1.000 77.7

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
Scolopia chinensis MN078144.1 157292 View on NCBI ↗
Scolopia saeva MN078143.1 155832 View on NCBI ↗