Markers + reference

Sedum

23 species · Crassulaceae · Saxifragales

Back to catalogue

Species 23
Genome length 149–151 kb
Candidate markers 273
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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 679 0.0636 0.96 80.1 yes View details
rps16-trnQ-UUG LSC 1382 0.0755 0.99 80.1 yes View details
trnS-GCU-trnG-GCC LSC 638 0.0580 0.95 82.2 yes View details
lhbA-trnG-UCC LSC 777 0.0700 0.90 79.5 yes View details
ycf1 IRb 1140 0.0093 1.00 47.1 no View details
ndhF-rpl32 SSC 615 0.0575 0.99 79.6 yes View details
rpl32-trnL-UAG SSC 489 0.0916 0.94 73.5 yes View details
ycf1 SSC 5169 0.0416 1.00 69.9 yes View details
trnT-GGU-psbD LSC 687 0.0513 0.99 81.1 yes View details
rpoB-trnC-GCA LSC 1145 0.0467 0.98 80.8 yes View details
trnC-GCA-petN LSC 879 0.0526 0.95 80.6 yes View details
psbM-trnD-GUC LSC 445 0.0448 0.99 80.6 yes View details
ndhC-trnV-UAC LSC 893 0.0449 0.98 80.4 yes View details
atpH-atpI LSC 682 0.0450 1.00 80.1 yes View details
trnG-UCC-trnfM-CAU LSC 146 0.0488 1.00 80.0 yes View details
psaJ-rpl33 LSC 423 0.0472 0.94 78.3 yes View details
accD-psaI LSC 563 0.0512 0.97 77.7 yes View details
psbE-petL LSC 1086 0.0392 0.97 77.0 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCCGTAGCAGGCACTAATA AAAAGGGTATGTTGCTGCCA 1558–1732 0.870 86.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGTCGTGGTCGTACAAAC AAAAGGGTATGTTGCTGCCA 1301–1476 0.870 85.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT AAAAGGGTATGTTGCTGCCA 1267–1442 0.826 84.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGTACAAACTCTACCGACGG AAAAGGGTATGTTGCTGCCA 1426–1465 0.696 78.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT TCTTGAGCTGTACGAAGGGA 896–1059 0.565 73.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1130–1484 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1141–1495 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1151–1505 1.000 88.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1152–1506 1.000 88.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 1153–1507 1.000 86.3
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 628–753 1.000 59.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 627–752 1.000 59.9
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCTCACTTTTACCACT 642–767 1.000 59.1
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCTCACTTTTACCACT 641–766 1.000 59.1
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 629–754 1.000 58.8
trnG-GCC_p1 trnG-GCC CAATCCGACGCTTTAGTCCA AGGAACAGTTGGAACGCTTT 1696–1889 1.000 91.5
trnG-GCC_p2 trnG-GCC AATCCGACGCTTTAGTCCAC AGGAACAGTTGGAACGCTTT 1695–1888 1.000 91.5
trnG-GCC_p3 trnG-GCC CAATCCGACGCTTTAGTCCA CAATGGACGCGTTTCATTCC 1535–1729 0.609 75.5
trnG-GCC_p4 trnG-GCC AATCCGACGCTTTAGTCCAC CAATGGACGCGTTTCATTCC 1534–1728 0.609 75.5
trnG-GCC_p5 trnG-GCC GTCACCTGACAAAAGGCAGA AGGAACAGTTGGAACGCTTT 1253–1307 0.304 56.4
atpH-atpI_p1 atpH-atpI ATGGGAAGGTTGGGGGAATA TCAACCGCTATCGCTATTCG 1552–1596 0.739 79.1
atpH-atpI_p2 atpH-atpI ATGGGAAGGTTGGGGGAATA AGTGGTTCCGATACCTGTCA 1097–1123 0.696 76.8
atpH-atpI_p3 atpH-atpI ATGGGAAGGTTGGGGGAATA TTAGGTTCAACCGCTATCGC 1558–1602 0.609 73.3
atpH-atpI_p4 atpH-atpI TTTGAATGGGAAGGTTGGGG TCAACCGCTATCGCTATTCG 1578–1587 0.348 54.8
atpH-atpI_p5 atpH-atpI TTTGAATGGGAAGGTTGGGG AGTGGTTCCGATACCTGTCA 1105–1114 0.348 54.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TTCCCTCATTTCCATCCCGG CCGGATTTGAACTGGGGAAA 1141–1246 1.000 79.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCCCTCATTTCCATCCCGG AAAAGGATTTGCAGTCCCCC 1123–1228 1.000 77.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTCCCTCATTTCCATCCCGG AGTCTTGTGTTGATCAGGCG 1165–1270 0.957 77.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCCCTCATTTCCATCCCGG GTCTTGTGTTGATCAGGCGA 1164–1269 0.957 77.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTCCCTCATTTCCATCCCGG TCTTGTGTTGATCAGGCGAC 1163–1268 0.957 77.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

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

Species Accession Length (bp) Link
Sedum adolphii NC_085688.1 150370 View on NCBI ↗
Sedum alfredii NC_064359.1 149427 View on NCBI ↗
Sedum annuum PP175354.1 150379 View on NCBI ↗
Sedum batesii NC_085698.1 150001 View on NCBI ↗
Sedum bulbiferum NC_065835.1 150074 View on NCBI ↗
Sedum clavatum NC_085689.1 150001 View on NCBI ↗
Sedum crassularia NC_085695.1 149653 View on NCBI ↗
Sedum emarginatum NC_054184.1 149188 View on NCBI ↗
Sedum japonicum PP234499.1 149397 View on NCBI ↗
Sedum japonicum subsp. oryzifolium NC_027837.1 149609 View on NCBI ↗
Sedum lineare NC_052707.1 149257 View on NCBI ↗
Sedum lushanense NC_087797.1 148691 View on NCBI ↗
Sedum morganianum NC_085692.1 150280 View on NCBI ↗
Sedum multiceps NC_085693.1 150503 View on NCBI ↗
Sedum pachyphyllum NC_071898.1 149960 View on NCBI ↗
Sedum plumbizincicola PP234488.1 149288 View on NCBI ↗
Sedum rubrotinctum NC_085694.1 149961 View on NCBI ↗
Sedum sarmentosum NC_023085.1 150448 View on NCBI ↗
Sedum sexangulare PP175358.1 149644 View on NCBI ↗
Sedum spiralifolium PP078685.1 149336 View on NCBI ↗
Sedum tricarpum MZ519883.1 149349 View on NCBI ↗
Sedum versadense NC_085696.1 149576 View on NCBI ↗
Sedum xunvense PV177150.1 149595 View on NCBI ↗