Markers + reference

Sempervivum

6 species · Crassulaceae · Saxifragales

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Species 6
Genome length 151–151 kb
Candidate markers 273
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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0011 1.00 32.5 yes View details
trnK-UUU-rps16 LSC 680 0.0167 0.97 64.9 yes View details
rps16-trnQ-UUG LSC 1536 0.0138 1.00 63.3 yes View details
trnS-GCU-trnG-GCC LSC 639 0.0166 0.93 63.7 yes View details
psbM-trnD-GUC LSC 991 0.0148 1.00 66.2 yes View details
petA-psbJ LSC 860 0.0137 1.00 56.8 yes View details
psbE-petL LSC 1025 0.0116 1.00 55.7 yes View details
ycf1 IRb 1078 0.0016 1.00 38.1 no View details
ndhF SSC 2208 0.0073 1.00 42.5 yes View details
ndhF-rpl32 SSC 600 0.0129 1.00 52.8 yes View details
ycf1 SSC 5166 0.0100 1.00 47.3 yes View details
trnH-GUG-psbA LSC 239 0.0477 0.99 74.5 yes View details
ycf4-cemA LSC 614 0.0135 1.00 64.0 yes View details
psbC-trnS-UGA LSC 183 0.0281 0.99 60.9 yes View details
trnG-GCC-trnR-UCU LSC 244 0.0158 0.98 59.4 yes View details
trnP-UGG-psaJ LSC 350 0.0134 0.99 58.9 yes View details
trnT-GGU-psbD LSC 676 0.0061 0.99 55.9 yes View details
psaC-ndhE SSC 276 0.0068 0.99 54.8 yes View details
trnD-GUC-trnY-GUA LSC 308 0.0119 1.00 54.0 yes View details
petL-petG LSC 172 0.0182 0.99 52.9 yes View details
trnL-UAA-trnF-GAA LSC 267 0.0162 1.00 52.5 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 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 ATTTCTTCCTAGCTGCGTGG 426–525 1.000 86.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ATTTCTTCCTAGCTGCGTGG 440–539 1.000 86.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC ATTTCTTCCTAGCTGCGTGG 439–538 1.000 86.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC ATTTCTTCCTAGCTGCGTGG 441–540 1.000 86.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGTGGCCTGTAGTTGGTATC 411–510 1.000 86.5
psbA_p1 psbA GATCCACTTGGCTACATCCG ACATAGGGAAAGCTGTGTGC 1602–1701 1.000 83.1
psbA_p2 psbA GATCCACTTGGCTACATCCG CATAGGGAAAGCTGTGTGCA 1601–1700 1.000 83.1
psbA_p3 psbA CAATCCACTGCCTTGATCCA ACATAGGGAAAGCTGTGTGC 1616–1715 1.000 83.0
psbA_p4 psbA CAATCCACTGCCTTGATCCA CATAGGGAAAGCTGTGTGCA 1615–1714 1.000 83.0
psbA_p5 psbA AATCCACTGCCTTGATCCAC ACATAGGGAAAGCTGTGTGC 1615–1714 1.000 83.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGGCGGATGTTTTTAGGGA 745–771 1.000 77.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGCGGATGTTTTTAGGGAA 744–770 1.000 77.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGGCGGATGTTTTTAGGGA 744–770 1.000 77.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGCGGATGTTTTTAGGGAA 743–769 1.000 77.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGCGGATGTTTTTAGGGAAC 742–768 1.000 77.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1149–1617 1.000 84.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAACTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1156–1624 0.833 75.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CTTCAACTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 1159–1627 0.833 75.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCAACTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 1157–1625 0.833 75.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTCAACTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 1158–1626 0.833 75.3
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 620–696 1.000 54.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 619–695 1.000 54.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA TACCACTAAACTATACCCGC 638–714 1.000 54.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCTCACTTTTACCACT 634–710 1.000 53.8
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCTCACTTTTACCACT 633–709 1.000 53.8
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGGTTTAGAAGACCTATGTCCT 308–331 1.000 49.8
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGAAGACCTATGTCCTATCCA 302–325 1.000 49.6
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT ACCAAAGGTTTAGAAGACCTATGT 313–336 1.000 49.2
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU TGACGTCGACTATAACCCCT AGGTTTAGAAGACCTATGTCCT 327–350 1.000 48.0
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU TGACGTCGACTATAACCCCT AGAAGACCTATGTCCTATCCA 321–344 1.000 47.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Sempervivum arachnoideum NC_085697.1 151133 View on NCBI ↗
Sempervivum calcareum PP262169.1 151456 View on NCBI ↗
Sempervivum ciliosum PP262170.1 151271 View on NCBI ↗
Sempervivum funckii PP262171.1 151145 View on NCBI ↗
Sempervivum heuffelii PP262173.1 150845 View on NCBI ↗
Sempervivum tectorum NC_053954.1 151182 View on NCBI ↗