Markers + reference

Withania

8 species · Solanaceae · Solanales

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Species 8
Genome length 154–157 kb
Candidate markers 270
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 451 0.0578 0.98 83.6 yes View details
rps16-trnQ LSC 1224 0.0246 0.98 68.5 yes View details
trnL-UAA-trnF-GAA LSC 300 0.0549 0.98 73.9 yes View details
petA-psbJ LSC 705 0.0439 1.00 77.0 yes View details
clpP LSC 2002 0.0189 1.00 59.0 yes View details
ycf1 IRb 1047 0.0051 1.00 48.4 no View details
ndhF-rpl32 SSC 809 0.0294 0.97 74.4 yes View details
rpl32-trnL-UAG SSC 855 0.0266 1.00 71.9 yes View details
ycf1 SSC 5670 0.0199 1.00 60.3 yes View details
trnE-UUC-trnT-GGU LSC 876 0.0159 0.99 68.8 yes View details
trnK-rps16 LSC 676 0.0254 0.99 65.4 yes View details
trnS-trnG LSC 629 0.0161 0.98 65.4 yes View details
petD-rpoA LSC 179 0.0383 1.00 62.5 yes View details
rpoB-trnC-GCA LSC 1313 0.0178 0.99 62.2 yes View details
rpl33-rps18 LSC 192 0.0434 0.89 62.0 yes View details
rps4-trnT-UGU LSC 364 0.0228 1.00 61.9 yes View details
rpl36-rps8 LSC 449 0.0314 0.98 61.7 yes View details
psaJ-rpl33 LSC 450 0.0186 0.96 60.3 yes View details
trnT-GGU-psbD LSC 1176 0.0136 1.00 60.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 475–521 1.000 90.4
trnH-psbA_p2 trnH-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 489–535 1.000 90.3
trnH-psbA_p3 trnH-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 488–534 1.000 90.3
trnH-psbA_p4 trnH-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 490–536 1.000 90.3
trnH-psbA_p5 trnH-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 524–570 1.000 88.3
trnK-rps16_p1 trnK-rps16 CCCTTTCAGGATCAGTCGTG AAAAGGGTATGTTGCTGCCA 1487–1509 0.875 78.9
trnK-rps16_p2 trnK-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGGTATGTTGCTGCCA 1486–1508 0.875 78.9
trnK-rps16_p3 trnK-rps16 TCCCTTTCAGGATCAGTCGT AAAAGGGTATGTTGCTGCCA 1488–1510 0.875 78.6
trnK-rps16_p4 trnK-rps16 TCAGGATCAGTCGTGGTCTT AAAAGGGTATGTTGCTGCCA 1482–1504 0.875 78.5
trnK-rps16_p5 trnK-rps16 TTCAGGATCAGTCGTGGTCT AAAAGGGTATGTTGCTGCCA 1483–1505 0.875 78.5
rps16-trnQ_p1 rps16-trnQ TGGCAGCAACATACCCTTTT GAGGTTCGAATCCTTCCGTC 1512–1715 1.000 88.2
rps16-trnQ_p2 rps16-trnQ TGGCAGCAACATACCCTTTT CTTACAGCAGCTTGCCAAAC 2076–2287 1.000 87.9
rps16-trnQ_p3 rps16-trnQ CCCTCGTGAAACACTTTGGA CTTACAGCAGCTTGCCAAAC 2018–2229 1.000 87.7
rps16-trnQ_p4 rps16-trnQ CCAATGATGTCGAGCCAAGA CTTACAGCAGCTTGCCAAAC 1880–1975 0.875 79.7
rps16-trnQ_p5 rps16-trnQ AGAACCAATGATGTCGAGCC CTTACAGCAGCTTGCCAAAC 1884–1979 0.875 79.7
trnS-trnG_p1 trnS-trnG ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 680–724 1.000 58.8
trnS-trnG_p2 trnS-trnG ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 683–727 1.000 57.8
trnS-trnG_p3 trnS-trnG ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 682–726 1.000 57.8
trnS-trnG_p4 trnS-trnG ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 729–773 1.000 57.7
trnS-trnG_p5 trnS-trnG ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 681–725 1.000 56.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TTGCGAAGTCTTGATAGCCC 2103–2136 1.000 84.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT GGCGCAGAGTCAAAAAGAAC 2478–2511 1.000 84.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TTCTGCTGGGGAATCATTCG 1950–1991 1.000 84.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGAAAATACCGGATCGCCAC TTGCGAAGTCTTGATAGCCC 2311–2344 1.000 84.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CAGAAAATACCGGATCGCCA TTGCGAAGTCTTGATAGCCC 2312–2345 1.000 84.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 985–1023 1.000 86.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 964–1002 1.000 85.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 961–999 1.000 85.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 947–985 1.000 85.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 982–1020 1.000 84.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Withania adpressa BK010847.2 154364 View on NCBI ↗
Withania coagulans NC_047176.1 154196 View on NCBI ↗
Withania echinata PV472659.1 156876 View on NCBI ↗
Withania frutescens NC_068894.1 153771 View on NCBI ↗
Withania heterophylla PV472656.1 156764 View on NCBI ↗
Withania japonica PV472660.1 156924 View on NCBI ↗
Withania riebeckii BK010849.2 154162 View on NCBI ↗
Withania somnifera NC_047245.1 155365 View on NCBI ↗