Markers + reference

Derris

2 species · Fabaceae · Fabales

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Species 2
Genome length 154–154 kb
Candidate markers 266
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

17 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf3 LSC 1981 0.0122 0.99 50.6 yes View details
rpoC2 LSC 4155 0.0082 1.00 44.4 yes View details
rpoC2-rps2 LSC 234 0.0812 1.00 73.5 yes View details
atpH-atpF LSC 566 0.0338 0.99 68.0 yes View details
trnG-UCC-psaI LSC 357 0.0393 1.00 69.3 yes View details
rps16-trnQ-UUG LSC 467 0.0368 0.93 70.3 yes View details
psaJ-rpl33 LSC 476 0.0449 0.98 74.4 yes View details
rps12-clpP LSC 210 0.0270 0.88 58.8 yes View details
clpP-psbB LSC 438 0.0365 1.00 68.4 yes View details
rpoA LSC 1002 0.0170 1.00 54.6 yes View details
rps11-rpl36 LSC 328 0.0411 0.96 70.0 yes View details
rpl36-rps8 LSC 506 0.0304 0.97 63.3 yes View details
rps3-rps19 LSC 445 0.0256 0.97 60.4 yes View details
ycf1 IRb 445 0.0067 1.00 47.5 no View details
ndhF-rpl32 SSC 714 0.0321 0.79 70.3 yes View details
ndhG-ndhI SSC 440 0.0393 0.98 64.7 yes View details
ycf1 SSC 5376 0.0177 1.00 48.5 yes View details
trnW-CCA-trnP-UGG LSC 23 0.0870 1.00 78.4 yes View details
trnH-GUG-psbA LSC 272 0.0480 0.92 74.6 yes View details
petD-rpoA LSC 184 0.0761 1.00 70.9 yes View details
rbcL-atpB LSC 804 0.0188 0.99 70.1 yes View details
rpl2-trnH-GUG LSC 110 0.0404 0.90 69.0 no View details
trnR-ACG-trnN-GUU IRb 638 0.0173 1.00 68.8 yes View details
trnN-GUU-trnR-ACG IRa 638 0.0173 1.00 68.8 yes View details
trnT-GGU-trnE-UUC LSC 827 0.0249 0.97 68.1 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 115 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 CCCTCTAGATCTAGCTGCGA 324–339 1.000 84.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCCCTCTAGATCTAGCTGCG 325–340 1.000 84.3
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCCTCTAGATCTAGCTGCGA 338–353 1.000 84.2
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCCCTCTAGATCTAGCTGCG 339–354 1.000 84.2
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCCTCTAGATCTAGCTGCGA 337–352 1.000 84.2
rbcL-atpB_p1 rbcL-atpB TTAACACCAGCCTTGAACCC CCTGGGGGAAAAGCTACATC 970–977 1.000 81.1
rbcL-atpB_p2 rbcL-atpB TTAACACCAGCCTTGAACCC CAAGTGCAGAAACCTCAGGA 903–910 1.000 79.6
rbcL-atpB_p3 rbcL-atpB TTAACACCAGCCTTGAACCC TCAAGTGCAGAAACCTCAGG 904–911 1.000 79.6
rbcL-atpB_p4 rbcL-atpB TTAACACCAGCCTTGAACCC AAGTGCAGAAACCTCAGGAC 902–909 1.000 79.6
rbcL-atpB_p5 rbcL-atpB CCTTGAACCCAACACTTGCT CCTGGGGGAAAAGCTACATC 960–967 1.000 76.4
ycf3_p1 ycf3 TAATGATGCCCAGAAACCGG TGACATAGGAGTTAGGCGCT 2904–2924 1.000 79.6
ycf3_p2 ycf3 TAATGATGCCCAGAAACCGG GCGCTTAACGGACCTTTTTG 2889–2909 1.000 78.8
ycf3_p3 ycf3 GCCCAGAAACCGGTTGAATA TGACATAGGAGTTAGGCGCT 2897–2917 1.000 78.6
ycf3_p4 ycf3 AAGGTTCGGAAAGAGAGGGA GCGCTTAACGGACCTTTTTG 2987 0.500 57.2
ycf3_p5 ycf3 TCGGAAAGAGAGGGATTCGA TGACATAGGAGTTAGGCGCT 2997 0.500 57.1
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT ACTGCCTTTCGTAGTACCCT 965–974 1.000 83.0
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC ACTGCCTTTCGTAGTACCCT 944–953 1.000 82.6
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC TGGCGTTACTCTACCACTGA ACTGCCTTTCGTAGTACCCT 941–950 1.000 82.4
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TTTCGTAGTACCCTACCCCC 959–968 1.000 82.2
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC CCGATGACTTACGCCTTACC ACTGCCTTTCGTAGTACCCT 962–971 1.000 81.8
rpoC2_p1 rpoC2 CTTCCCTTCCGGTATCTCGA TGAACTTCCTCGGGAATGAA 246 1.000 67.2
rpoC2_p2 rpoC2 TCTTCCCTTCCGGTATCTCG TGAACTTCCTCGGGAATGAA 247 1.000 67.2
rpoC2_p3 rpoC2 TCCCTTCCGGTATCTCGATT TGAACTTCCTCGGGAATGAA 244 1.000 66.7
rpoC2_p4 rpoC2 TTCCCTTCCGGTATCTCGAT TGAACTTCCTCGGGAATGAA 245 1.000 66.7
rpoC2_p5 rpoC2 CCCTTCCGGTATCTCGATTG TGAACTTCCTCGGGAATGAA 243 1.000 66.2
rpoC2-rps2_p1 rpoC2-rps2 TGTGATACATCAGAACAATATAGGGT CCTGCTTCCATCATCTCTTCC 314–318 1.000 44.8
rpoC2-rps2_p2 rpoC2-rps2 TGTGATACATCAGAACAATATAGGGT ACTCCTGCTTCCATCATCTCT 317–321 1.000 44.8
rpoC2-rps2_p3 rpoC2-rps2 TGTGATACATCAGAACAATATAGGGT TGAACTCCTGCTTCCATCATC 320–324 1.000 44.7
rpoC2-rps2_p4 rpoC2-rps2 TGTGATACATCAGAACAATATAGGGT CCGTGACCAAAATGAACTCC 332–336 1.000 44.6
rpoC2-rps2_p5 rpoC2-rps2 TGTGATACATCAGAACAATATAGGGT TGACCAAAATGAACTCCTGCT 329–333 1.000 44.6

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
Derris ferruginea PV870835.1 153558 View on NCBI ↗
Derris harrowiana NC_057446.1 153846 View on NCBI ↗