Markers + reference

Capparis

6 species · Capparaceae · Brassicales

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Species 6
Genome length 158–158 kb
Candidate markers 267
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 383 0.0439 0.97 70.7 yes View details
trnK-UUU-rps16 LSC 967 0.0228 0.97 60.8 yes View details
trnR-UCU-atpA LSC 282 0.0312 0.97 64.6 yes View details
trnT-UGU-trnL-UAA LSC 852 0.0182 0.99 64.3 yes View details
petA-psbJ LSC 1116 0.0239 1.00 51.2 yes View details
rpl16-rps3 LSC 1277 0.0222 0.99 66.7 yes View details
rpl32-trnL-UAG SSC 1158 0.0305 1.00 76.7 yes View details
ccsA-ndhD SSC 329 0.0379 1.00 66.1 yes View details
ycf1 SSC 5511 0.0156 1.00 55.7 yes View details
ndhF-rpl32 SSC 531 0.0240 0.94 65.8 yes View details
trnF-GAA-ndhJ LSC 597 0.0233 0.99 63.3 yes View details
trnS-CGA-trnR-UCU LSC 226 0.0286 1.00 63.1 yes View details
rbcL-accD LSC 685 0.0159 0.99 61.7 yes View details
trnR-ACG-trnN-GUU IRb 624 0.0115 1.00 61.7 yes View details
atpH-atpI LSC 1073 0.0150 0.94 61.5 yes View details
psbF-psbE LSC 9 0.0370 1.00 61.4 yes View details
rpl36-rps8 LSC 494 0.0256 0.97 60.9 yes View details
trnS-UGA-psbZ LSC 351 0.0279 1.00 60.5 yes View details
trnE-UUC-trnT-GGU LSC 796 0.0154 0.99 60.2 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 95 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 ATTTCAGGCTGAGCACAACA 902–923 1.000 84.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCAGGCTGAGCACAACATT 900–921 1.000 84.3
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTTCAGGCTGAGCACAACAT 901–922 1.000 84.3
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCAGGCTGAGCACAACATT 914–935 1.000 84.2
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTTCAGGCTGAGCACAACAT 915–936 1.000 84.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 1133–1199 1.000 87.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAAAAGGCGCTCAACCTACA 1129–1195 1.000 87.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT AAAAAGGCGCTCAACCTACA 1130–1196 1.000 87.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1271–1337 1.000 87.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 1272–1338 1.000 87.2
trnS-CGA-trnR-UCU_p1 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 301–310 1.000 70.4
trnS-CGA-trnR-UCU_p2 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 304–313 1.000 70.1
trnS-CGA-trnR-UCU_p3 trnS-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 307–316 1.000 69.6
trnS-CGA-trnR-UCU_p4 trnS-CGA-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 310–319 1.000 69.3
trnS-CGA-trnR-UCU_p5 trnS-CGA-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 305–314 1.000 67.9
trnR-UCU-atpA_p1 trnR-UCU-atpA AGTGAAAAGCGTCCATTGTCT CTACCAAGGCATTCACCGAA 445–494 1.000 77.1
trnR-UCU-atpA_p2 trnR-UCU-atpA AGTGAAAAGCGTCCATTGTCT TACCAAGGCATTCACCGAAG 444–493 1.000 77.1
trnR-UCU-atpA_p3 trnR-UCU-atpA AGTGAAAAGCGTCCATTGTCT TTCTACCAAGGCATTCACCG 447–496 1.000 77.1
trnR-UCU-atpA_p4 trnR-UCU-atpA GTGAAAAGCGTCCATTGTCT CTACCAAGGCATTCACCGAA 444–493 1.000 75.5
trnR-UCU-atpA_p5 trnR-UCU-atpA GTGAAAAGCGTCCATTGTCT TACCAAGGCATTCACCGAAG 443–492 1.000 75.5
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TACAAGCGGGATTCAAGCTC 1108–1182 1.000 85.9
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TACAAGCGGGATTCAAGCTC 1166–1240 1.000 85.7
atpH-atpI_p3 atpH-atpI GTCCAATAGAAGCAAGCCCA TACAAGCGGGATTCAAGCTC 1148–1222 1.000 85.6
atpH-atpI_p4 atpH-atpI GCTGTACCTTGACCAACTCC TACAAGCGGGATTCAAGCTC 1170–1244 1.000 85.0
atpH-atpI_p5 atpH-atpI AACGGAAGCAGCAGAAATCA GCGGGATTCAAGCTCTCATT 1103–1177 1.000 83.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 921–962 1.000 84.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 900–941 1.000 83.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 897–938 1.000 83.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 883–924 1.000 83.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 862–903 1.000 83.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Capparis cartilaginea PP706108.1 157727 View on NCBI ↗
Capparis decidua NC_053386.1 157573 View on NCBI ↗
Capparis spinosa MT041701.1 157728 View on NCBI ↗
Capparis spinosa var. inermis PP706112.1 157857 View on NCBI ↗
Capparis spinosa var. ovata NC_049616.1 157783 View on NCBI ↗
Capparis spinosa var. spinosa NC_047193.1 157796 View on NCBI ↗