Markers + reference

Graptopetalum

2 species · Crassulaceae · Saxifragales

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Species 2
Genome length 150–150 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1072 0.0150 1.00 54.6 yes View details
rps16-trnQ-UUG LSC 1411 0.0130 0.98 68.1 yes View details
trnS-GCU-trnG-GCC LSC 629 0.0159 1.00 65.3 yes View details
atpH LSC 246 0.0081 1.00 45.4 yes View details
trnC-GCA-petN LSC 850 0.0141 1.00 61.0 yes View details
ycf1 IRb 1161 0.0034 1.00 46.9 no View details
ndhD SSC 1503 0.0040 1.00 47.9 yes View details
ycf1 SSC 5211 0.0071 1.00 57.0 yes View details
ndhD-psaC SSC 132 0.1591 1.00 77.5 yes View details
trnH-GUG-psbA LSC 159 0.0252 1.00 64.9 yes View details
trnD-GUC-trnY-GUA LSC 312 0.0161 1.00 62.3 yes View details
rpl20-rps12 LSC 1106 0.0071 0.77 62.3 yes View details
rpl36-infA LSC 120 0.0167 1.00 62.1 yes View details
psbE-petL LSC 1085 0.0028 0.98 62.0 yes View details
trnR-ACG-trnN-GUU IRb 592 0.0051 1.00 61.5 yes View details
trnN-GUU-trnR-ACG IRa 592 0.0051 1.00 61.5 yes View details
ndhE-ndhG SSC 179 0.0114 0.98 61.2 yes View details
ycf3 LSC 1995 0.0035 0.99 60.6 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 CTGCCTTAATCCACTTGGCT GTAACGCTCACAACTTCCCT 250–252 1.000 78.9
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC GTAACGCTCACAACTTCCCT 251–253 1.000 78.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TGAACGTAACGCTCACAACT 255–257 1.000 78.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TGAACGTAACGCTCACAACT 256–258 1.000 78.3
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ATGCATGAACGTAACGCTCA 260–262 1.000 77.9
trnK-UUU_p1 trnK-UUU GGACTCCCAAGCAACCAAAT TCGAATGCAATTTGTTGCCC 2985–2986 1.000 77.1
trnK-UUU_p2 trnK-UUU GGACTCCCAAGCAACCAAAT CGAATGCAATTTGTTGCCCT 2984–2985 1.000 77.0
trnK-UUU_p3 trnK-UUU GGACTCCCAAGCAACCAAA TCGAATGCAATTTGTTGCCC 2985–2986 1.000 71.0
trnK-UUU_p4 trnK-UUU GGACTCCCAAGCAACCAAA CGAATGCAATTTGTTGCCCT 2984–2985 1.000 71.0
trnK-UUU_p5 trnK-UUU GACTCCCAAGCAACCAAATT TCGAATGCAATTTGTTGCCC 2984–2985 1.000 68.0
rps16_p1 rps16 GAGTTAGCAACCCCAAACCA CGGGACTCAAAACTGTGGAT 2003–2014 1.000 80.0
rps16_p2 rps16 TGAGTTAGCAACCCCAAACC CGGGACTCAAAACTGTGGAT 2004–2015 1.000 80.0
rps16_p3 rps16 GAGTTAGCAACCCCAAACCA AGTTGAATTCTTCGTGCGGA 1907–1913 1.000 79.9
rps16_p4 rps16 TGAGTTAGCAACCCCAAACC AGTTGAATTCTTCGTGCGGA 1908–1914 1.000 79.9
rps16_p5 rps16 GAGTTAGCAACCCCAAACCA ACGAATTTCACCACGTACCC 1882 0.500 58.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1483–1484 1.000 80.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1494–1495 1.000 80.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ATAAATCGAAGTGGGGCGTG 1542–1543 1.000 78.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1504–1505 1.000 78.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1505–1506 1.000 78.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TGTTCGGAATACAAAGAAAACCG 753–764 1.000 56.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TGTTCGGAATACAAAGAAAACCG 752–763 1.000 56.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA TGTTCGGAATACAAAGAAAACCG 771–782 1.000 55.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACTATTAGG 732–743 1.000 55.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACTATTAGG 731–742 1.000 55.3
atpH_p1 atpH TGTAGTTTTTAGTTAGATTTCTAGGA TTTTGGTGCGAGGAACTTCT 298 1.000 40.5
atpH_p2 atpH TGTAGTTTTTAGTTAGATTTCTAGG TTTTGGTGCGAGGAACTTCT 298 1.000 40.5
atpH_p3 atpH ATGTAGTTTTTAGTTAGATTTCTAGGA TTTTGGTGCGAGGAACTTCT 299 1.000 40.5
atpH_p4 atpH TGTAGTTTTTAGTTAGATTTCTAGGAT TTTTGGTGCGAGGAACTTCT 298 1.000 40.5
atpH_p5 atpH GTAGTTTTTAGTTAGATTTCTAGGA TTTTGGTGCGAGGAACTTCT 297 1.000 40.5

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
Graptopetalum amethystinum NC_053950.1 150365 View on NCBI ↗
Graptopetalum paraguayense MN064718.1 150040 View on NCBI ↗