Markers + reference

Crassula

12 species · Crassulaceae · Saxifragales

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Species 12
Genome length 145–146 kb
Candidate markers 274
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 580 0.0678 0.99 77.6 yes View details
rps16-trnQ-UUG LSC 1241 0.0601 0.95 76.4 yes View details
psbM-trnD-GUC LSC 927 0.0470 0.99 81.3 yes View details
psbZ-trnG-GCC LSC 585 0.0640 1.00 81.5 yes View details
trnF-GAA-ndhJ LSC 671 0.0659 0.98 76.7 yes View details
rbcL-accD LSC 662 0.0554 1.00 78.7 yes View details
psbE-petL LSC 1021 0.0505 1.00 83.4 yes View details
ycf1 IRb 1084 0.0128 1.00 49.1 no View details
rps15-ycf1 SSC 331 0.0683 1.00 73.2 yes View details
ycf1 SSC 5019 0.0420 1.00 68.3 yes View details
trnS-GCU-trnG-UCC LSC 546 0.0555 0.99 79.9 yes View details
petN-psbM LSC 1019 0.0401 0.99 76.3 yes View details
trnT-GGU-psbD LSC 728 0.0433 1.00 75.9 yes View details
petA-psbJ LSC 771 0.0471 0.97 75.6 yes View details
atpH-atpI LSC 443 0.0657 0.98 75.4 yes View details
trnH-GUG-psbA LSC 301 0.0870 0.92 75.2 yes View details
rpoB-trnC-GCA LSC 790 0.0393 1.00 74.9 yes View details
ndhF-rpl32 SSC 546 0.0553 1.00 74.9 yes View details
trnR-UCU-atpA LSC 138 0.0763 0.93 74.0 yes View details
psaI-pafII LSC 421 0.0446 0.99 73.2 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 GATCCACTTGGCTACATCCG AGCTGCTGTTGAAGTTCCAT 339–377 1.000 88.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTGCTGTTGAAGTTCCAT 353–391 1.000 88.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCTGTTGAAGTTCCAT 352–390 1.000 88.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCTGTTGAAGTTCCAT 354–392 1.000 88.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCTGCTGTTGAAGTTCCATC 338–376 1.000 86.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGTCGTGGTCGTACAAAC TCTATCCCAATGAGCCGTCT 928–1150 1.000 90.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CAGTCGTGGTCGTACAAACT TCTATCCCAATGAGCCGTCT 927–1149 1.000 90.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCTATCCCAATGAGCCGTCT 842–1064 1.000 89.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGGCTTCTTCTACACAACCA TCTATCCCAATGAGCCGTCT 1277–1320 0.750 74.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACGGCTTCTTCTACACAACC TCTATCCCAATGAGCCGTCT 1278–1321 0.750 74.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CTAGATCCTTGCCCCTGAGA CTTACAGCAGCTTGCCAAAC 1758–2044 0.833 84.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CTAGATCCTTGCCCCTGAGA GAGGTTCGAATCCTTCCGTC 1214–1499 0.833 84.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCCTTGCCCCTGAGAACTAA GAGGTTCGAATCCTTCCGTC 1294–1494 0.833 80.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCTTGCCCCTGAGAACTAA CTTACAGCAGCTTGCCAAAC 1839–2039 0.833 79.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCTTGCCCCTGAGAACTAA GTGTTCGCGCACCTATCTAA 1971–2171 0.667 72.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 588–606 1.000 59.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 587–605 1.000 59.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCTCACTTTTACCACT 602–620 1.000 59.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCTCACTTTTACCACT 601–619 1.000 59.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 589–607 1.000 58.8
trnR-UCU-atpA_p1 trnR-UCU-atpA CCCTTCTATGGGGGTCATCT ATCTGTCCAAGCAAGCACAA 1329–1380 1.000 87.8
trnR-UCU-atpA_p2 trnR-UCU-atpA CCTCAAGATTCTCGCCACTC ATCTGTCCAAGCAAGCACAA 1391–1401 0.833 76.3
trnR-UCU-atpA_p3 trnR-UCU-atpA CCTCAAGATTCTCGCCACTC ACTGACGAAGCAAAAACCCT 734–742 0.667 70.2
trnR-UCU-atpA_p4 trnR-UCU-atpA CCCTTCTATGGGGGTCATCT ACTGACGAAGCAAAAACCCT 672–680 0.667 70.0
trnR-UCU-atpA_p5 trnR-UCU-atpA CCTCAAGATTCTCGCCACTC CACTGACGAAGCAAAAACCC 735–743 0.667 69.6
atpH-atpI_p1 atpH-atpI GCAGCAATAACAGAAGCAGC GAATACGGTCCTTGGGTTCC 950–1152 1.000 89.7
atpH-atpI_p2 atpH-atpI GCAGCAATAACAGAAGCAGC TCAACCGCTATCGCTATTCG 1061–1263 1.000 89.4
atpH-atpI_p3 atpH-atpI GGGTTGTCTCGCAATACCTT GAATACGGTCCTTGGGTTCC 1041–1243 1.000 89.4
atpH-atpI_p4 atpH-atpI AAGAAGGGGCAGGAAAAAGG GAATACGGTCCTTGGGTTCC 1321–1331 0.833 76.0
atpH-atpI_p5 atpH-atpI AAGAAGGGGCAGGAAAAAGG TCAACCGCTATCGCTATTCG 1432–1442 0.833 75.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Crassula alstonii NC_081503.1 145507 View on NCBI ↗
Crassula capitella NC_085681.1 145866 View on NCBI ↗
Crassula columella NC_081504.1 145554 View on NCBI ↗
Crassula dejecta NC_081505.1 145870 View on NCBI ↗
Crassula expansa subsp. fragilis OP882299.1 144969 View on NCBI ↗
Crassula mesembrianthemopsis NC_085268.1 146046 View on NCBI ↗
Crassula mesembryanthoides NC_081506.1 146057 View on NCBI ↗
Crassula perforata NC_053949.1 145737 View on NCBI ↗
Crassula rupestris subsp. marnieriana OM935751.1 145737 View on NCBI ↗
Crassula socialis NC_081507.1 145842 View on NCBI ↗
Crassula tecta NC_081508.1 146060 View on NCBI ↗
Crassula volkensii NC_085270.1 144855 View on NCBI ↗