Markers + reference

Pachyphytum

2 species · Crassulaceae · Saxifragales

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Species 2
Genome length 149–150 kb
Candidate markers 272
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 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1403 0.0116 0.98 62.3 yes View details
trnS-GCU-trnG-GCC LSC 635 0.0142 1.00 61.7 yes View details
trnG-GCC-trnR-UCU LSC 234 0.0478 0.89 76.5 yes View details
rps2-rpoC2 LSC 310 0.0199 0.97 56.1 yes View details
ycf1 IRb 1140 0.0018 1.00 53.5 no View details
ndhF SSC 2217 0.0059 1.00 53.5 yes View details
ccsA SSC 960 0.0052 1.00 47.4 yes View details
ccsA-ndhD SSC 251 0.0440 1.00 72.7 yes View details
ycf1 SSC 5172 0.0096 0.95 48.1 yes View details
psbF-psbE LSC 9 0.1111 1.00 87.5 yes View details
rps19-rpl2 IRb 54 0.0370 1.00 73.8 yes View details
trnL-UAG-ccsA SSC 73 0.0278 0.99 69.8 yes View details
trnF-GAA-ndhJ LSC 648 0.0125 0.99 66.8 yes View details
trnC-GCA-petN LSC 867 0.0084 0.96 66.1 yes View details
psaA-ycf3 LSC 675 0.0047 0.96 65.7 yes View details
accD-psaI LSC 560 0.0108 0.99 65.0 yes View details
psbZ-trnG-UCC LSC 727 0.0057 0.97 64.8 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1450–1476 1.000 80.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1461–1487 1.000 80.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ATAAATCGAAGTGGGGCGTG 1509–1535 1.000 78.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1471–1497 1.000 78.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1472–1498 1.000 78.3
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TGTTCGGAATACAAAGAAAACCG 759–761 1.000 56.3
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TGTTCGGAATACAAAGAAAACCG 758–760 1.000 56.3
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA TGTTCGGAATACAAAGAAAACCG 777–779 1.000 55.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACTATTAGG 738–740 1.000 55.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACTATTAGG 737–739 1.000 55.5
trnG-GCC_p1 trnG-GCC GTCACCTGACAAAAGGCAGA AGGAACAGTTGGAACGCTTT 1253–1281 1.000 82.0
trnG-GCC_p2 trnG-GCC CAATCCGACGCTTTAGTCCA AGGAACAGTTGGAACGCTTT 1816–1842 1.000 81.9
trnG-GCC_p3 trnG-GCC AATCCGACGCTTTAGTCCAC AGGAACAGTTGGAACGCTTT 1815–1841 1.000 81.8
trnG-GCC_p4 trnG-GCC CAATCCGACGCTTTAGTCCA CAATGGACGCGTTTCATTCC 1682 0.500 59.1
trnG-GCC_p5 trnG-GCC AATCCGACGCTTTAGTCCAC CAATGGACGCGTTTCATTCC 1681 0.500 59.1
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA AGGTTTAGAAGACCTATGTCCT 324–348 1.000 50.0
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGGTTTAGAAGACCTATGTCCT 297–321 1.000 49.9
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA AGAAGACCTATGTCCTATCCA 318–342 1.000 49.8
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGAAGACCTATGTCCTATCCA 291–315 1.000 49.7
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU TCCTGAGTTGACGTCGACTA ACCAAAGGTTTAGAAGACCTATGT 329–353 1.000 49.4
rps2-rpoC2_p1 rps2-rpoC2 ACCAAAATGAACTCCCGCTT ACATCAGAACAATCATTTCTGGG 412–423 1.000 51.4
rps2-rpoC2_p2 rps2-rpoC2 AATGAACTCCCGCTTCCATC ACATCAGAACAATCATTTCTGGG 407–418 1.000 51.1
rps2-rpoC2_p3 rps2-rpoC2 CCCGCTTCCATCATCTCTTC ACATCAGAACAATCATTTCTGGG 399–410 1.000 50.5
rps2-rpoC2_p4 rps2-rpoC2 CCGCTTCCATCATCTCTTCC ACATCAGAACAATCATTTCTGGG 398–409 1.000 50.5
rps2-rpoC2_p5 rps2-rpoC2 ATATAAGGTGCCATTCGCGG ACATCAGAACAATCATTTCTGGG 453–464 1.000 49.6
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 899–932 1.000 81.3
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAACCAGCCCAAGCAAGA 905–938 1.000 79.8
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TAAACCAGCCCAAGCAAGAC 904–937 1.000 79.7
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCAAGACTTACT 917–950 1.000 79.1
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAGAGTCCACTTCGTCCCC 961–994 1.000 79.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Pachyphytum compactum NC_053953.1 149339 View on NCBI ↗
Pachyphytum longifolium NC_068662.1 150179 View on NCBI ↗