Markers + reference

Tapeinosperma

2 species · Primulaceae · Ericales

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Species 2
Genome length 155–155 kb
Candidate markers 265
Primer pairs 95

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 427 0.0070 1.00 59.2 yes View details
psbK-psbI LSC 394 0.0051 1.00 57.4 yes View details
atpH-atpI LSC 602 0.0066 1.00 62.6 yes View details
rpoC2 LSC 4185 0.0007 1.00 51.9 yes View details
rbcL LSC 1428 0.0021 1.00 60.0 yes View details
ycf1 IRb 992 0.0000 1.00 25.0 no View details
ndhF SSC 2223 0.0027 1.00 48.1 yes View details
ndhF-rpl32 SSC 968 0.0108 0.95 69.4 yes View details
ccsA SSC 978 0.0010 1.00 51.5 yes View details
ccsA-ndhD SSC 249 0.0442 1.00 77.9 yes View details
ycf1 SSC 5592 0.0022 0.90 57.2 yes View details
trnR-UCU-atpA LSC 124 0.0161 1.00 61.8 yes View details
petB LSC 1407 0.0028 1.00 60.4 yes View details
ycf4-cemA LSC 735 0.0027 1.00 60.3 yes View details
rpoA LSC 1008 0.0020 1.00 59.9 yes View details
rps16 LSC 1113 0.0018 1.00 59.8 yes View details
rpoB-trnC-GCA LSC 1139 0.0018 1.00 59.8 yes View details
psaA-ycf3 LSC 664 0.0015 1.00 59.6 yes View details
rpl20-rps12 LSC 790 0.0013 1.00 59.6 yes View details
trnT-UGU-trnL-UAA LSC 812 0.0012 1.00 59.5 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 95 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 558 1.000 79.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 503 1.000 78.8
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 504 1.000 78.6
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 496 1.000 77.2
trnH-GUG-psbA_p5 trnH-GUG-psbA TTAGTTATGGGCGAACGACG TAGACCTAGCTGCGGTTGAA 551 1.000 76.2
rps16_p1 rps16 AGTAGGGAAGTGATGACTCGT TCAATTCCATACCGGTTCCA 1225 1.000 59.6
rps16_p2 rps16 AGTAGGGAAGTGATGACTCGT TCAATTCCATACCGGTTCCAA 1225 1.000 57.6
rps16_p3 rps16 AGTAGGGAAGTGATGACTCGT ATCAATTCCATACCGGTTCCA 1226 1.000 55.9
rps16_p4 rps16 GTAGGGAAGTGATGACTCGT TCAATTCCATACCGGTTCCA 1224 1.000 55.3
rps16_p5 rps16 AGTAGGGAAGTGATGACTCGT TCAATTCCATACCGGTTCCAAA 1225 1.000 55.1
psbK-psbI_p1 psbK-psbI GCTGCTGTAAGTTTTCGCTG AGGATTACGCCCTGGATCAT 511 1.000 77.8
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGATTACGCCCTGGATCAT 520 1.000 77.7
psbK-psbI_p3 psbK-psbI AGCTGCTGTAAGTTTTCGCT AGGATTACGCCCTGGATCAT 512 1.000 77.3
psbK-psbI_p4 psbK-psbI TATGCCAGTCATCCCTCTGT AGGATTACGCCCTGGATCAT 560 1.000 76.7
psbK-psbI_p5 psbK-psbI GCCAGTCATCCCTCTGTTTT AGGATTACGCCCTGGATCAT 557 1.000 76.5
trnR-UCU-atpA_p1 trnR-UCU-atpA CGGAATGAATGAAAAGCGTCC GCTATTCAGGAACAGACGGA 259–268 1.000 63.2
trnR-UCU-atpA_p2 trnR-UCU-atpA CGGAATGAATGAAAAGCGTCC AGCTATTCAGGAACAGACGG 260–269 1.000 63.1
trnR-UCU-atpA_p3 trnR-UCU-atpA CGGAATGAATGAAAAGCGTCC GGAAGCCCTTTTGAAAGAAGC 278–287 1.000 62.6
trnR-UCU-atpA_p4 trnR-UCU-atpA CCAAACAAGAGGCAAAATCGG GCTATTCAGGAACAGACGGA 277–286 1.000 62.3
trnR-UCU-atpA_p5 trnR-UCU-atpA CCAAACAAGAGGCAAAATCGG AGCTATTCAGGAACAGACGG 278–287 1.000 62.2
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTGCAACTTTAGCCGCTG 687 1.000 78.6
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCTG 745 1.000 78.5
atpH-atpI_p3 atpH-atpI CAGCAGCAATAACAGAAGCG TTTTGCAACTTTAGCCGCTG 697 1.000 78.0
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC TTTTGCAACTTTAGCCGCTG 749 1.000 77.8
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCT TTTTGCAACTTTAGCCGCTG 727 1.000 76.0
rpoC2_p1 rpoC2 TTCTCGTGGAGAATGGCAAG GATGTGTATCATGCGCCTGA 332 1.000 78.6
rpoC2_p2 rpoC2 TTCTCGTGGAGAATGGCAAG TACCGATGTGTATCATGCGC 336 1.000 77.9
rpoC2_p3 rpoC2 TTCTCGTGGAGAATGGCAAG ATGTGTATCATGCGCCTGAA 331 1.000 77.0
rpoC2_p4 rpoC2 TTCTCGTGGAGAATGGCAAG TGTGTATCATGCGCCTGAAT 330 1.000 77.0
rpoC2_p5 rpoC2 TCGTGGAGAATGGCAAGATC GATGTGTATCATGCGCCTGA 329 1.000 76.9

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
Tapeinosperma multiflorum NC_045117.1 155168 View on NCBI ↗
Tapeinosperma netor NC_045118.1 154616 View on NCBI ↗