Markers + reference

Hyoscyamus

2 species · Solanaceae · Solanales

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Species 2
Genome length 156–156 kb
Candidate markers 256
Primer pairs 85

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 256 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5670 0.3300 0.87 75.1 yes View details
ndhH SSC 1182 0.5054 0.87 81.3 yes View details
ndhA SSC 2215 0.4799 0.90 80.6 yes View details
psaC SSC 246 0.5284 0.72 70.7 yes View details
ndhD SSC 1503 0.4665 0.82 80.1 yes View details
ccsA SSC 942 0.4350 0.73 77.3 yes View details
ndhF SSC 2223 0.4646 0.83 78.8 yes View details
ycf1 IRa 1458 0.0096 1.00 49.4 no View details
trnL(UAG)-rpl32 SSC 880 0.4495 0.85 80.9 yes View details
rpl32-ndhF SSC 766 0.4431 0.85 80.7 yes View details
ndhI SSC 504 0.4527 0.86 79.2 yes View details
ndhE-psaC SSC 251 0.4306 0.86 76.9 yes View details
ndhG-ndhE SSC 159 0.4658 0.92 76.5 yes View details
ndhD-ccsA SSC 231 0.5142 0.92 76.5 yes View details
ycf1-rps15 SSC 396 0.4251 0.84 76.3 yes View details
ndhE SSC 306 0.4746 0.90 76.1 yes View details
rpl32 SSC 168 0.4568 0.96 76.0 yes View details
ndhI-ndhG SSC 413 0.4405 0.81 75.9 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf1_p1 ycf1 ACACTCGGAATATTTCATTCGGA TGGGCGCGTTGGAATTATAA 421 0.500 35.5
ycf1_p2 ycf1 ACACTCGGAATATTTCATTCGGA TTGGGCGCGTTGGAATTATA 422 0.500 35.5
ycf1_p3 ycf1 ACACTCGGAATATTTCATTCGGA ATCGATCTTAACCCAGGCCT 588 0.500 34.3
ycf1_p4 ycf1 ACACTCGGAATATTTCATTCGGA GGATCACCGGGCATATCAAA 452 0.500 33.7
ycf1_p5 ycf1 ACACTCGGAATATTTCATTCGG TGGGCGCGTTGGAATTATAA 421 0.500 32.4
ycf1-rps15_p1 ycf1-rps15 TGAATTGGAATGGCGTCGAT AGTCGTTGACGTTTTCCCAA 829 0.500 59.5
ycf1-rps15_p2 ycf1-rps15 TGAATTGGAATGGCGTCGAT GCCTAATTGTTCGGGTCCAT 1303 0.500 59.3
ycf1-rps15_p3 ycf1-rps15 TGAATTGGAATGGCGTCGAT ATGAGTCGAAGAACACCGTG 1119 0.500 59.2
ycf1-rps15_p4 ycf1-rps15 TGAATTGGAATGGCGTCGAT CCAACGTGTTACATAGGGCA 1243 0.500 58.9
ycf1-rps15_p5 ycf1-rps15 TGAATTGGAATGGCGTCGAT AGCTATCCGACTCAACTCCA 1369 0.500 58.5
ndhH_p1 ndhH TTGGGAAAACGTCAACGACT GAAGTCCAACAGGAGCAACA 1843 0.500 59.5
ndhH_p2 ndhH TTGGGAAAACGTCAACGACT CACCAATGCTAAGATCGGCT 1798 0.500 59.5
ndhH_p3 ndhH TTGGGAAAACGTCAACGACT ATTCAGGTCCGATACGTTGC 1603 0.500 59.3
ndhH_p4 ndhH TTGGGAAAACGTCAACGACT GGAGCAACACTTGAAATGGC 1832 0.500 59.2
ndhH_p5 ndhH TTGGGAAAACGTCAACGACT AAAGGGCCAGCATATTCAGG 1616 0.500 59.2
ndhA_p1 ndhA GTGAGAGTTGAAGCCCCAAA TCAAAGTGTATTCGGCCTCG 2680 0.500 59.8
ndhA_p2 ndhA GCAACGAGAAGGGGATTCAT TCAAAGTGTATTCGGCCTCG 2909 0.500 59.6
ndhA_p3 ndhA CAGGCTCTGGAAGGAATTCC TCAAAGTGTATTCGGCCTCG 2833 0.500 59.6
ndhA_p4 ndhA GTGAGAGTTGAAGCCCCAAA CGTGGGACAGGGTAATCATG 2598 0.500 59.5
ndhA_p5 ndhA GCAACGAGAAGGGGATTCAT CGTGGGACAGGGTAATCATG 2827 0.500 59.3
ndhI_p1 ndhI CGATGGGCACAGTGATGTTA TCCATCTCCTACGGTCCAAA 1868 0.500 57.9
ndhI_p2 ndhI CGATGGGCACAGTGATGTTA TTCCATCTCCTACGGTCCAA 1869 0.500 57.9
ndhI_p3 ndhI GATGGACTTTACCGAGGCTG TCCATCTCCTACGGTCCAAA 1414 0.500 57.6
ndhI_p4 ndhI GATGGACTTTACCGAGGCTG TTCCATCTCCTACGGTCCAA 1415 0.500 57.6
ndhI_p5 ndhI AGATGGACTTTACCGAGGCT TCCATCTCCTACGGTCCAAA 1415 0.500 57.0
ndhI-ndhG_p1 ndhI-ndhG CGAGGCCGAATACACTTTGA TCCATCTCCTACGGTCCAAA 1052 0.500 58.0
ndhI-ndhG_p2 ndhI-ndhG CGAGGCCGAATACACTTTGA TTCCATCTCCTACGGTCCAA 1053 0.500 58.0
ndhI-ndhG_p3 ndhI-ndhG CATGATTACCCTGTCCCACG TCCATCTCCTACGGTCCAAA 1134 0.500 57.7
ndhI-ndhG_p4 ndhI-ndhG CATGATTACCCTGTCCCACG TTCCATCTCCTACGGTCCAA 1135 0.500 57.7
ndhI-ndhG_p5 ndhI-ndhG GATGGACTTTACCGAGGCTG TCCATCTCCTACGGTCCAAA 1414 0.500 57.6

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
Hyoscyamus muticus MZ450974.1 156271 View on NCBI ↗
Hyoscyamus niger NC_024261.1 155720 View on NCBI ↗