Markers + reference

Phedimus

13 species · Crassulaceae · Saxifragales

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Species 13
Genome length 150–152 kb
Candidate markers 275
Primer pairs 90

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 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1513 0.0291 1.00 68.9 yes View details
trnS-GCU-trnG-GCC LSC 629 0.0347 1.00 71.2 yes View details
trnG-GCC-trnR-UCU LSC 313 0.0596 0.98 67.8 yes View details
rpoB-trnC-GCA LSC 1136 0.0258 1.00 66.3 yes View details
trnE-UUC-trnT-GGU LSC 288 0.0310 1.00 50.0 yes View details
ycf4-cemA LSC 603 0.0296 1.00 64.1 yes View details
ycf1 IRb 1197 0.0045 1.00 39.2 no View details
ndhF SSC 2226 0.0180 1.00 53.8 yes View details
ycf1 SSC 5169 0.0228 1.00 54.6 yes View details
trnH-GUG-psbA LSC 281 0.0477 1.00 71.6 yes View details
petA-psbJ LSC 991 0.0281 1.00 70.3 yes View details
ndhF-rpl32 SSC 505 0.0313 1.00 67.7 yes View details
psbZ-trnG-GCC LSC 701 0.0189 0.99 65.6 yes View details
trnC-GCA-petN LSC 841 0.0222 1.00 64.0 yes View details
trnK-UUU-rps16 LSC 655 0.0249 1.00 63.4 yes View details
ndhC-trnV-UAC LSC 880 0.0208 1.00 63.4 yes View details
trnT-GGU-psbD LSC 702 0.0259 1.00 63.3 yes View details
rps2-rpoC2 LSC 253 0.0323 0.99 63.2 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 90 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 275–354 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 289–368 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 288–367 1.000 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 290–369 1.000 90.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 278–357 1.000 90.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA CCCAATGAGCCGTTTATCGA 924–986 1.000 88.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA TCCCAATGAGCCGTTTATCG 925–987 1.000 88.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC CCCAATGAGCCGTTTATCGA 925–987 1.000 88.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC TCCCAATGAGCCGTTTATCG 926–988 1.000 88.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT CCCAATGAGCCGTTTATCGA 927–989 1.000 88.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGTTCGAATCCTTCCGTCC 1309–1601 1.000 82.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTCGAATCCTTCCGTCCC 1308–1600 1.000 82.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGAATCCTTCCGTCCCA 1307–1599 1.000 80.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AGGTTCGAATCCTTCCGTCC 1310–1602 1.000 79.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGAATCCTTCCGTCCCAG 1307–1599 1.000 79.2
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACCACTAAACTATACCCGCT 578–717 1.000 73.1
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACCACTAAACTATACCCGCT 577–716 1.000 73.1
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA ACCACTAAACTATACCCGCT 596–735 1.000 72.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACCACTAAACTATACCCGCT 632–771 1.000 72.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AGCTCGTACAACGGATTAGC ACCACTAAACTATACCCGCT 597–736 1.000 71.5
trnG-GCC_p1 trnG-GCC CAATCCGACGCTTTAGTCCA ATGGACGCGTTTCATTACGA 1656–1791 1.000 92.0
trnG-GCC_p2 trnG-GCC CAATCCGACGCTTTAGTCCA TGGACGCGTTTCATTACGAT 1655–1790 1.000 92.0
trnG-GCC_p3 trnG-GCC AATCCGACGCTTTAGTCCAC TGGACGCGTTTCATTACGAT 1654–1789 1.000 91.9
trnG-GCC_p4 trnG-GCC GCCGGGCCTTTTCAAAATAC ATGGACGCGTTTCATTACGA 1406–1535 0.846 83.5
trnG-GCC_p5 trnG-GCC GCCGGGCCTTTTCAAAATAC TGGACGCGTTTCATTACGAT 1405–1534 0.846 83.5
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA AGGTTTAGAAGACCTATGTCCT 412–438 1.000 55.6
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA AGAAGACCTATGTCCTATCCA 406–432 1.000 55.4
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGGTTTAGAAGACCTATGTCCT 385–411 1.000 55.3
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGAAGACCTATGTCCTATCCA 379–405 1.000 55.1
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA ACCAAAGGTTTAGAAGACCTATGT 417–443 1.000 55.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Phedimus aizoon NC_068773.1 151757 View on NCBI ↗
Phedimus aizoon var. floribundus OP344945.1 151748 View on NCBI ↗
Phedimus ellacombeanus NC_068772.1 151869 View on NCBI ↗
Phedimus kamtschaticus NC_037946.1 151652 View on NCBI ↗
Phedimus kurilensis NC_068771.1 151845 View on NCBI ↗
Phedimus litoralis NC_068769.1 151761 View on NCBI ↗
Phedimus middendorffianus NC_068768.1 151557 View on NCBI ↗
Phedimus odontophyllus NC_063948.1 150000 View on NCBI ↗
Phedimus selskianus NC_068767.1 151768 View on NCBI ↗
Phedimus sikokianus NC_068766.1 151769 View on NCBI ↗
Phedimus spurius NC_063950.1 151004 View on NCBI ↗
Phedimus yangshanicus NC_063949.1 150000 View on NCBI ↗
Phedimus zokuriensis NC_068765.1 151746 View on NCBI ↗