Markers + reference

Cadaba

2 species · Capparaceae · Brassicales

Back to catalogue

Species 2
Genome length 156–157 kb
Candidate markers 275
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 408 0.0380 0.97 79.5 yes View details
trnK-UUU-rps16 LSC 964 0.0189 0.99 71.0 yes View details
trnR-UCU-atpA LSC 239 0.0441 0.95 69.6 yes View details
rpoB-trnC-GCA LSC 1119 0.0136 0.99 60.1 yes View details
psaJ-rpl33 LSC 442 0.0252 0.99 57.1 yes View details
ycf1 IRb 1029 0.0010 1.00 44.8 no View details
ndhF SSC 2247 0.0107 1.00 55.8 yes View details
ndhF-rpl32 SSC 968 0.0374 0.97 72.0 yes View details
ccsA-ndhD SSC 287 0.0559 1.00 75.3 yes View details
ndhA SSC 2169 0.0092 1.00 59.6 yes View details
ycf1 SSC 5388 0.0113 1.00 44.9 yes View details
trnW-CCA-trnP-UGG LSC 192 0.0365 1.00 73.5 yes View details
trnS-CGA-trnR-UCU LSC 205 0.0406 0.96 73.0 yes View details
atpF-atpH LSC 518 0.0178 0.98 69.5 yes View details
rps14-psaB LSC 151 0.0214 0.93 68.8 yes View details
rps8-rpl14 LSC 259 0.0207 0.93 67.8 yes View details
petN-psbM LSC 643 0.0202 1.00 65.1 yes View details
trnS-GCU-trnS-CGA LSC 598 0.0118 0.99 64.5 yes View details
infA LSC 108 0.0370 1.00 63.9 yes View details
psaA-ycf3 LSC 666 0.0105 1.00 63.5 yes View details
trnR-ACG-trnN-GUU IRb 625 0.0080 1.00 63.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 472–478 1.000 83.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 486–492 1.000 82.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 485–491 1.000 82.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 487–493 1.000 82.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGAGGCTCCATCCACAAATG 449–455 1.000 82.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AACTCTACCGCAGATCTGGA AAAAAGGCGCTCAACCTACA 1161–1166 1.000 80.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 AACTCTACCGCAGATCTGGA AGAAGGCAGGGGTTTTTACG 1119–1124 1.000 80.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AACTCTACCGCAGATCTGGA CGCTCAACCTACAGGAACAG 1154–1159 1.000 78.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AAAAAGGCGCTCAACCTACA 1104–1109 1.000 77.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AACTCTACCGCAGATCTGGA GGCAGGGGTTTTTACGGAAT 1115–1120 1.000 77.5
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA TGAATCAAACCGAGAGACCC 712–761 1.000 75.1
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC TGAATCAAACCGAGAGACCC 711–760 1.000 75.0
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA ACGGAAAGAGAGGGATTCGA TGAATCAAACCGAGAGACCC 766–815 1.000 73.8
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA GAATCAAACCGAGAGACCCT 711–760 1.000 72.7
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC GAATCAAACCGAGAGACCCT 710–759 1.000 72.7
trnS-CGA-trnR-UCU_p1 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 284–286 1.000 67.8
trnS-CGA-trnR-UCU_p2 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 287–289 1.000 67.6
trnS-CGA-trnR-UCU_p3 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 290–292 1.000 67.1
trnS-CGA-trnR-UCU_p4 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 293–295 1.000 66.8
trnS-CGA-trnR-UCU_p5 trnS-CGA-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 288–290 1.000 65.3
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACGTTTTCTACTTCAGGAACA 289–297 1.000 46.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GAACGTTTTCTACTTCAGGAACA 291–299 1.000 46.0
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AACGTTTTCTACTTCAGGAACA 290–298 1.000 46.0
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACGTTTTCTACTTCAGGAACAA 289–297 1.000 46.0
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT ACGTTTTCTACTTCAGGAACA 324–332 1.000 45.4
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 627–636 1.000 78.4
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAGTAAACGA TGGCCTGGTTGTAGCATTAG 600–609 1.000 75.1
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TTTATGGCCTGGTTGTAGCA 631–640 1.000 74.6
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCCTGGTTGTAGCATTAGC 626–635 1.000 73.9
atpF-atpH_p5 atpF-atpH GGCCAGTGACCCAAGTAAAC TGGCCTGGTTGTAGCATTAG 602–611 1.000 73.4

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
Cadaba farinosa NC_058237.1 156481 View on NCBI ↗
Cadaba glandulosa NC_058238.1 156560 View on NCBI ↗