Markers + reference

Pseudosedum

2 species · Crassulaceae · Saxifragales

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Species 2
Genome length 151–151 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-trnQ-UUG LSC 1453 0.1335 0.94 85.4 yes View details
trnS-GCU-trnG-GCC LSC 631 0.1252 0.96 84.4 yes View details
rpoB-trnC-GCA LSC 1116 0.1064 0.84 79.6 yes View details
trnC-GCA-petN LSC 840 0.1046 0.77 76.3 yes View details
petN-psbM LSC 799 0.1007 0.96 82.6 yes View details
psbE-petL LSC 1036 0.1279 0.97 85.8 yes View details
ycf1 IRb 1091 0.0121 0.99 52.2 no View details
ycf1 SSC 5208 0.0834 0.99 71.7 yes View details
psbM-trnD-GUC LSC 1014 0.0918 0.96 84.3 yes View details
ndhF-rpl32 SSC 620 0.1115 0.93 84.2 yes View details
psaA-ycf3 LSC 661 0.0817 0.93 82.8 yes View details
petA-psbJ LSC 932 0.0919 0.98 82.3 yes View details
rpl32-trnL-UAG SSC 482 0.1068 0.95 81.8 yes View details
ndhC-trnV-UAC LSC 779 0.0736 0.98 81.4 yes View details
trnK-UUU-rps16 LSC 643 0.1065 0.98 81.1 yes View details
petG-trnW-CCA LSC 126 0.0909 0.96 81.1 yes View details
atpF-atpH LSC 401 0.1090 0.94 80.8 yes View details
atpH-atpI LSC 678 0.0889 1.00 80.4 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_p1 trnK-UUU CTACTGGAGGAGCTGCAATG GTGTGGCAGGCAATTTTGAG 2999 0.500 57.9
trnK-UUU_p2 trnK-UUU ATAGGCTTTCAGTTTCGCGT GAGTGTGGCAGGCAATTTTG 2866 0.500 57.5
trnK-UUU_p3 trnK-UUU ATAGGCTTTCAGTTTCGCGT GTGTGGCAGGCAATTTTGAG 2864 0.500 57.5
trnK-UUU_p4 trnK-UUU AAACGACCCCATAGGCTTTC GAGTGTGGCAGGCAATTTTG 2876 0.500 57.3
trnK-UUU_p5 trnK-UUU AAACGACCCCATAGGCTTTC GTGTGGCAGGCAATTTTGAG 2874 0.500 57.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CATTTCGGATCAGTCGTGGT AAAAGGGTATGTTGCTGCCA 1420–1444 1.000 87.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA AAAAGGGTATGTTGCTGCCA 1374–1398 1.000 87.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC AAAAGGGTATGTTGCTGCCA 1375–1399 1.000 87.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT AAAAGGGTATGTTGCTGCCA 1377–1401 1.000 87.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGCCATTCCCATTTCGGATC AAAAGGGTATGTTGCTGCCA 1429 0.500 59.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1518–1531 1.000 85.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1521–1534 1.000 82.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CACGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 1520–1533 1.000 79.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CACGTTGCTTTCTACCACAT GAGGTTCGAATCCTTCCGTC 1520–1533 1.000 78.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCACGTTGCTTTCTACCAC GAGGTTCGAATCCTTCCGTC 1521–1534 1.000 77.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 680–686 1.000 58.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 679–685 1.000 58.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA TACCACTAAACTATACCCGC 698–704 1.000 58.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 681–687 1.000 57.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TTACCACTAAACTATACCCGC 680–686 1.000 57.6
atpF-atpH_p1 atpF-atpH ACAGAATCGGTTACGTTTTTCA ATTTGCAAATCCCTTTGTTT 422–446 1.000 51.6
atpF-atpH_p2 atpF-atpH ACAGAATCGGTTACGTTTTTCAT ATTTGCAAATCCCTTTGTTT 422–446 1.000 51.6
atpF-atpH_p3 atpF-atpH ACAGAATCGGTTACGTTTTTCA TTTGCAAATCCCTTTGTTTAA 421–445 1.000 51.6
atpF-atpH_p4 atpF-atpH CAGAATCGGTTACGTTTTTCA ATTTGCAAATCCCTTTGTTT 421–445 1.000 51.6
atpF-atpH_p5 atpF-atpH ACAGAATCGGTTACGTTTTTCA CTTTTATTTGCAAATCCCTTTGT 427–451 1.000 51.5
atpH-atpI_p1 atpH-atpI TCCAGCAGCAATAACGGAAG TAGGAGAATCGATGGAGGGC 749–772 1.000 81.6
atpH-atpI_p2 atpH-atpI AATCCAGCAGCAATAACGGA TAGGAGAATCGATGGAGGGC 751–774 1.000 80.3
atpH-atpI_p3 atpH-atpI ATCCAGCAGCAATAACGGAA TAGGAGAATCGATGGAGGGC 750–773 1.000 80.3
atpH-atpI_p4 atpH-atpI TAACGGAAGCAGCAGAAACC TAGGAGAATCGATGGAGGGC 738–761 1.000 79.9
atpH-atpI_p5 atpH-atpI GCAGCAGAAACCAGTGGATT TAGGAGAATCGATGGAGGGC 730–753 1.000 77.9

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
Pseudosedum affine PP975594.1 150617 View on NCBI ↗
Pseudosedum lievenii PP975595.1 151227 View on NCBI ↗