Markers + reference

Kalanchoe

14 species · Crassulaceae · Saxifragales

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Species 14
Genome length 150–151 kb
Candidate markers 267
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 677 0.0330 1.00 72.2 yes View details
rps16-trnQ-UUG LSC 1096 0.0397 0.98 78.5 yes View details
trnS-GCU-trnG-GCC LSC 602 0.0346 0.99 75.5 yes View details
petN-psbM LSC 1063 0.0343 0.84 67.2 yes View details
psbM-trnD-GUC LSC 1000 0.0272 0.97 73.9 yes View details
trnE-UUC-trnT-GGU LSC 752 0.0311 0.83 68.4 yes View details
lhbA-trnG-UCC LSC 644 0.0419 0.82 72.6 yes View details
petA-psbJ LSC 851 0.0360 0.81 71.7 yes View details
ndhF-rpl32 SSC 494 0.0357 0.96 70.6 yes View details
ccsA-ndhD SSC 253 0.0699 0.93 74.5 yes View details
ycf1 SSC 5154 0.0207 1.00 52.1 yes View details
trnH-GUG-psbA LSC 290 0.0512 0.93 76.9 yes View details
rpl32-trnL-UAG SSC 455 0.0343 1.00 74.8 yes View details
rbcL-accD LSC 658 0.0274 1.00 69.6 yes View details
ndhC-trnV-UAC LSC 860 0.0206 1.00 69.4 yes View details
ndhG-ndhI SSC 233 0.0576 0.97 67.8 yes View details
rpl2-trnH-GUG IRa 164 0.0125 0.99 66.9 no View details
trnS-GGA-rps4 LSC 213 0.0458 0.94 66.5 yes View details
rps2-rpoC2 LSC 236 0.0388 0.95 66.3 yes View details
trnG-GCC-trnR-UCU LSC 238 0.0334 0.89 66.1 yes View details
rpl20-rps12 LSC 785 0.0130 0.98 64.1 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 100 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 335–369 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 349–383 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 348–382 1.000 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 350–384 1.000 90.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 338–372 1.000 90.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCGAATTGGAGCTAAAGGGC AAAAGGGTATGTTGCTGCCA 1617–1673 1.000 88.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGAATTGGAGCTAAAGGGCT AAAAGGGTATGTTGCTGCCA 1616–1672 1.000 88.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TGGCTTTTTGTTTCCCTCGA AAAAGGGTATGTTGCTGCCA 1633–1689 1.000 87.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGTGGTCGTACAAAC AAAAGGGTATGTTGCTGCCA 1449–1500 1.000 87.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTTTCCCTCGAATTGGAGCT AAAAGGGTATGTTGCTGCCA 1624–1680 1.000 87.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1169–1560 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1180–1571 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTATGCGGAGGTTCGAATCC 1176–1567 1.000 89.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTATGCGGAGGTTCGAATCC 1187–1578 1.000 88.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TATGCGGAGGTTCGAATCCT 1175–1566 1.000 86.2
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 629–668 1.000 59.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 628–667 1.000 59.9
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCTCACTTTTACCACT 643–682 1.000 59.1
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCTCACTTTTACCACT 642–681 1.000 59.1
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 630–669 1.000 58.8
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT ATGGCAATAAACTGCGTCCA 339–367 1.000 86.9
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA ATGGCAATAAACTGCGTCCA 366–394 1.000 86.8
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AATCCTGAGTTGACGTCGAC ATGGCAATAAACTGCGTCCA 368–396 1.000 85.4
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA TGGCAATAAACTGCGTCCAA 365–393 1.000 85.0
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU TGACGTCGACTATAACCCCT ATGGCAATAAACTGCGTCCA 358–386 1.000 84.9
rps2-rpoC2_p1 rps2-rpoC2 GCCATTCTCGGATTCCACTT GTTGAGAGTTGGAACGAGCA 985–1012 1.000 85.7
rps2-rpoC2_p2 rps2-rpoC2 GGCTACTGAATCAGCTGCTT GTTGAGAGTTGGAACGAGCA 1145–1172 1.000 85.1
rps2-rpoC2_p3 rps2-rpoC2 GCCATTCTCGGATTCCACTT CAGAGCAGATTCAGCCCTTT 352–358 0.357 57.7
rps2-rpoC2_p4 rps2-rpoC2 AAGGTGCCATTCTCGGATTC CAGAGCAGATTCAGCCCTTT 357–363 0.357 57.6
rps2-rpoC2_p5 rps2-rpoC2 GGCTACTGAATCAGCTGCTT CAGAGCAGATTCAGCCCTTT 512–518 0.357 56.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Kalanchoe beharensis PQ063992.1 150357 View on NCBI ↗
Kalanchoe bracteata PQ041255.1 150560 View on NCBI ↗
Kalanchoe daigremontiana NC_053542.1 150058 View on NCBI ↗
Kalanchoe delagoensis MW237833.1 150018 View on NCBI ↗
Kalanchoe fedtschenkoi NC_053951.1 150001 View on NCBI ↗
Kalanchoe longiflora MW237836.1 149978 View on NCBI ↗
Kalanchoe millotii PQ063987.1 150003 View on NCBI ↗
Kalanchoe orgyalis PQ041254.1 150600 View on NCBI ↗
Kalanchoe prasina PQ063988.1 149988 View on NCBI ↗
Kalanchoe spathulata PQ063986.1 149922 View on NCBI ↗
Kalanchoe tomentosa MN794319.1 150757 View on NCBI ↗
Kalanchoe x edwardii PQ063991.1 151159 View on NCBI ↗
Kalanchoe x gildenhuysii PQ063990.1 149781 View on NCBI ↗
Kalanchoe x houghtonii PQ063989.1 150062 View on NCBI ↗