Markers + reference

Rhipsalis

2 species · Cactaceae · Caryophyllales

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Species 2
Genome length 122–122 kb
Candidate markers 218
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 218 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petN-psbM Genome 676 0.1698 0.78 80.7 yes View details
trnM-CAU-accD Genome 561 0.3184 0.91 82.0 yes View details
accD Genome 3072 0.1985 0.89 78.8 yes View details
rps7-trnL-CAA Genome 2483 0.1246 0.86 81.8 yes View details
clpP Genome 633 0.1320 0.98 81.3 yes View details
rps16-trnQ-UUG Genome 260 0.0545 0.99 81.2 yes View details
trnI-GAU-rrn16 Genome 306 0.1365 0.89 79.9 yes View details
trnI-CAU-trnH-GUG Genome 196 0.0745 0.82 77.0 yes View details
rpoC1-rpoB Genome 29 0.1034 1.00 74.8 yes View details
trnA-UGC-trnI-GAU Genome 60 0.0909 0.92 74.3 yes View details
trnS-GCU-clpP Genome 424 0.0597 0.91 73.7 yes View details
ycf1 Genome 5730 0.0756 0.97 73.6 yes View details
rrn16-trnV-GAC Genome 277 0.0970 0.86 73.6 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 65 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 333–485 1.000 81.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 344–496 1.000 81.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 363–515 1.000 80.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TAAGGCATCGGGTTTTGGTC 374–526 1.000 80.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTAAGGCATCGGGTTTTGGT 364–516 1.000 78.3
trnS-GCU-clpP_p1 trnS-GCU-clpP ACGGAAAGAGAGGGATTCGA TATCCTAGCGTGAGGGAGTG 853–891 1.000 88.7
trnS-GCU-clpP_p2 trnS-GCU-clpP ACGGAAAGAGAGGGATTCGA ATTCTCCTCCGACCAAGACA 818–856 1.000 88.5
trnS-GCU-clpP_p3 trnS-GCU-clpP ACGGAAAGAGAGGGATTCGA TTCTCCTCCGACCAAGACAT 817–855 1.000 88.5
trnS-GCU-clpP_p4 trnS-GCU-clpP ACGGAAAGAGAGGGATTCGA CTTGTTAGATCACGCCACGA 596 0.500 58.7
trnS-GCU-clpP_p5 trnS-GCU-clpP ACGGAAAGAGAGGGATTCGA TTGTTAGATCACGCCACGAG 595 0.500 58.7
clpP_p1 clpP TCTCCCTCCCCATGGAAAAT ACCCGCTACAGTTCCCTTAT 1205 1.000 89.8
clpP_p2 clpP TCTCCCTCCCCATGGAAAAT ATACCCGCTACAGTTCCCTT 1207 1.000 89.7
clpP_p3 clpP TCTCCCTCCCCATGGAAAAT CCAAATCTAAGACGGGACCG 1798 0.500 59.5
clpP_p4 clpP TCCGACTATTCTCATGGCCT CCAAATCTAAGACGGGACCG 1689 0.500 58.8
clpP_p5 clpP GACTATTCTCATGGCCTGGC CCAAATCTAAGACGGGACCG 1686 0.500 58.6
rpoC1-rpoB_p1 rpoC1-rpoB TGGCCCAAGCACTTATTTGT TCCAGATTAATAGGATGGAAGCT 128 1.000 46.3
rpoC1-rpoB_p2 rpoC1-rpoB TGTGGCCCAAGCACTTATTT TCCAGATTAATAGGATGGAAGCT 130 1.000 46.3
rpoC1-rpoB_p3 rpoC1-rpoB TTGTGGCCCAAGCACTTATT TCCAGATTAATAGGATGGAAGCT 131 1.000 46.2
rpoC1-rpoB_p4 rpoC1-rpoB TTTGTGGCCCAAGCACTTAT TCCAGATTAATAGGATGGAAGCT 132 1.000 46.2
rpoC1-rpoB_p5 rpoC1-rpoB TTTTGTGGCCCAAGCACTTA TCCAGATTAATAGGATGGAAGCT 133 1.000 44.5
petN-psbM_p1 petN-psbM ATTGTAAGTCTCGCTTGGGC AAAACGGTTAGCCAAAATGA 656–784 1.000 57.8
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT AAAACGGTTAGCCAAAATGA 594–722 1.000 57.0
petN-psbM_p3 petN-psbM ATTGTAAGTCTCGCTTGGGC AAACGGTTAGCCAAAATGAT 655–783 1.000 55.8
petN-psbM_p4 petN-psbM ATTGTAAGTCTCGCTTGGGC AACGGTTAGCCAAAATGATT 654–782 1.000 55.8
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT AACGGTTAGCCAAAATGATT 592–720 1.000 55.1
trnM-CAU-accD_p1 trnM-CAU-accD TACGCCTTAACGACCAATGG TAATTTGTCGACGTCGGTCC 1651 0.500 59.7
trnM-CAU-accD_p2 trnM-CAU-accD TACGCCTTAACGACCAATGG ATATAACGGCCCATTTGCGT 1781 0.500 59.7
trnM-CAU-accD_p3 trnM-CAU-accD TACGCCTTAACGACCAATGG GCAGAGTCTTTAGGGCCTTC 1379 0.500 59.6
trnM-CAU-accD_p4 trnM-CAU-accD TACGCCTTAACGACCAATGG TTTCTTGTCTGTGTTCCGCA 1422 0.500 59.6
trnM-CAU-accD_p5 trnM-CAU-accD TACGCCTTAACGACCAATGG TTTTGCCGTCTCTGTTGACA 1302 0.500 59.6

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
Rhipsalis baccifera NC_053545.1 122333 View on NCBI ↗
Rhipsalis teres NC_057526.1 122389 View on NCBI ↗