Markers + reference

Orostachys

10 species · Crassulaceae · Saxifragales

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Species 10
Genome length 150–151 kb
Candidate markers 268
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0055 1.00 41.5 yes View details
rps16-trnQ-UUG LSC 1267 0.0269 0.97 68.7 yes View details
trnC-GCA-petN LSC 831 0.0333 0.97 65.7 yes View details
ycf4-cemA LSC 611 0.0567 0.97 79.8 yes View details
petA-psbJ LSC 941 0.0335 0.99 72.1 yes View details
ycf1 IRb 1089 0.0046 1.00 37.5 no View details
ndhF-rpl32 SSC 604 0.0246 0.95 63.8 yes View details
rpl32-trnL-UAG SSC 439 0.0402 0.97 69.2 yes View details
ycf1 SSC 5154 0.0218 0.99 50.3 yes View details
trnH-GUG-psbA LSC 246 0.0624 0.97 74.7 yes View details
ndhG-ndhI SSC 242 0.0500 1.00 70.5 yes View details
ndhC-trnV-UAC LSC 886 0.0162 0.98 63.7 yes View details
rps3-rpl22 LSC 108 0.0504 0.98 62.0 yes View details
trnK-UUU-rps16 LSC 661 0.0179 0.99 61.2 yes View details
psbM-trnD-GUC LSC 1004 0.0189 1.00 59.6 yes View details
atpF-atpH LSC 382 0.0211 0.99 59.3 yes View details
petN-psbM LSC 1042 0.0191 0.98 59.2 yes View details
trnT-GGU-psbD LSC 717 0.0194 0.97 58.9 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 306–318 1.000 88.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 309–321 1.000 88.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 320–332 1.000 88.1
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 319–331 1.000 88.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 321–333 1.000 88.1
psbA_p1 psbA ACTCGTATAGACTAATACCGAAGT ATTTGGTTGCTTGGGAGTCC 1136 1.000 41.1
psbA_p2 psbA AACTCGTATAGACTAATACCGAAGT ATTTGGTTGCTTGGGAGTCC 1137 1.000 41.1
psbA_p3 psbA ACTCGTATAGACTAATACCGAAGTT ATTTGGTTGCTTGGGAGTCC 1136 1.000 41.1
psbA_p4 psbA ACTCGTATAGACTAATACCGAAG ATTTGGTTGCTTGGGAGTCC 1136 1.000 41.1
psbA_p5 psbA CTCGTATAGACTAATACCGAAGT ATTTGGTTGCTTGGGAGTCC 1135 1.000 41.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AGGGAACTTTTTCTTAATCAATCA 759–780 1.000 45.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC AGGGAACTTTTTCTTAATCAATCA 760–781 1.000 45.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGTACAAACTCTACCGACGG AGGGAACTTTTTCTTAATCAATCA 785–806 1.000 45.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC AGGGAACTTTTTCTTAATCAATCA 777–785 0.900 39.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT AGGGAACTTTTTCTTAATCAATCA 775–783 0.900 39.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1327–1364 1.000 85.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1338–1375 1.000 85.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTATGCGGAGGTTCGAATCC 1334–1371 1.000 84.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTATGCGGAGGTTCGAATCC 1345–1382 1.000 84.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TATGCGGAGGTTCGAATCCT 1333–1370 1.000 81.6
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG CGAGGCGGAGGGAAAAATAA 547–570 1.000 85.5
atpF-atpH_p2 atpF-atpH GGATGACCAGTGACCCAAAT CGAGGCGGAGGGAAAAATAA 526–549 1.000 82.4
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCGGAGGGAAAAATAAGAGGT 543–566 1.000 77.8
atpF-atpH_p4 atpF-atpH TATTAAACCCGAAACTCCCGG CGAGGCGGAGGGAAAAATAA 548–571 1.000 76.3
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG GAGGCGGAGGGAAAAATAAGA 546–569 1.000 75.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 879–902 1.000 87.0
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 873–896 1.000 85.5
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 897–920 1.000 84.6
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCAAGACTTACT 891–914 1.000 83.2
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAGAGTCCACTTCGTCCCC 935–958 1.000 83.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Orostachys chongsunensis NC_068863.1 151399 View on NCBI ↗
Orostachys fimbriata NC_053952.1 151195 View on NCBI ↗
Orostachys japonica NC_059698.1 150464 View on NCBI ↗
Orostachys japonica var. polycephala ON979327.1 150464 View on NCBI ↗
Orostachys latielliptica NC_068859.1 151462 View on NCBI ↗
Orostachys malacophylla NC_068861.1 151374 View on NCBI ↗
Orostachys malacophylla var. iwarenge NC_068862.1 151431 View on NCBI ↗
Orostachys malacophylla var. ramosa ON979330.1 151424 View on NCBI ↗
Orostachys margaritifolia NC_068860.1 151112 View on NCBI ↗
Orostachys minuta NC_063662.1 150368 View on NCBI ↗