Markers + reference

Aphragmus

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 149–153 kb
Candidate markers 270
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-CAA LSC 360 0.0615 0.99 70.2 yes View details
trnR-AGA-atpA LSC 294 0.0692 0.88 73.0 yes View details
ndhC-trnV-GUA LSC 662 0.0619 1.00 74.1 yes View details
accD LSC 1455 0.0364 1.00 65.2 yes View details
psaJ-rpl33 LSC 429 0.0847 0.99 75.2 yes View details
ndhF SSC 2232 0.0527 0.31 58.2 yes View details
rpl32-trnL-CUA SSC 761 0.0690 0.84 75.3 yes View details
ccsA-ndhD SSC 511 0.2795 0.86 79.5 yes View details
ndhD SSC 1227 0.2386 0.85 80.9 yes View details
trnH-CAC-psbA LSC 217 0.1058 0.96 86.9 yes View details
trnG-GGA-trnR-AGA LSC 147 0.1277 0.96 81.5 yes View details
trnS-AGC-trnG-GGA LSC 661 0.0583 0.96 80.1 yes View details
psaA-ycf3 LSC 722 0.0440 0.98 80.1 yes View details
petN-psbM LSC 541 0.0598 0.99 78.7 yes View details
psbC-trnS-UCA LSC 179 0.1011 0.99 78.1 yes View details
psbF-psbE LSC 9 0.2222 1.00 77.5 yes View details
trnT-ACC-psbD LSC 1237 0.0472 0.96 76.9 yes View details
trnfM-AUG-rps14 LSC 162 0.0688 0.99 76.4 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
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 275–278 1.000 87.5
trnH-CAC-psbA_p2 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 276–279 1.000 87.2
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 290–293 1.000 86.9
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 293–296 1.000 86.7
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 291–294 1.000 86.7
rps16-trnQ-CAA_p1 rps16-trnQ-CAA TCGAGCCAAGAGTGCCTATA CTTACAGCTGCTTGCCAAAC 1090 0.500 59.0
rps16-trnQ-CAA_p2 rps16-trnQ-CAA TCGAGCCAAGAGTGCCTATA GAGGTTCGAATCCTTCCGTC 527 0.500 58.9
rps16-trnQ-CAA_p3 rps16-trnQ-CAA CACAGCAGGTAAGGTCCTTC CTTACAGCTGCTTGCCAAAC 1021 0.500 58.7
rps16-trnQ-CAA_p4 rps16-trnQ-CAA TCGAGCCAAGAGTGCCTATA GATTCAAAAACGCGTAGGCC 1017 0.500 58.6
rps16-trnQ-CAA_p5 rps16-trnQ-CAA TCGAGCCAAGAGTGCCTATA GGATTCAAAAACGCGTAGGC 1018 0.500 58.6
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GGAACGAATCACACTTTTACCA 729–734 1.000 60.9
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC GGAACGAATCACACTTTTACCA 727–732 1.000 60.6
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GGAACGAATCACACTTTTACCAC 729–734 1.000 59.8
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC GGAACGAATCACACTTTTACCAC 727–732 1.000 59.5
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AGGAACGAATCACACTTTTACCA 730–735 1.000 59.3
trnG-GGA-trnR-AGA_p1 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 269 1.000 54.3
trnG-GGA-trnR-AGA_p2 trnG-GGA-trnR-AGA ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 275 1.000 54.1
trnG-GGA-trnR-AGA_p3 trnG-GGA-trnR-AGA AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 277 1.000 53.7
trnG-GGA-trnR-AGA_p4 trnG-GGA-trnR-AGA CGACGTCGACTAAAACCCTT TGATATTGCGTCCAATAGGA 289 1.000 53.6
trnG-GGA-trnR-AGA_p5 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 270 1.000 53.3
trnR-AGA-atpA_p1 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC GGAACGTTTTCTACTTCAGGAGA 378–404 1.000 54.7
trnR-AGA-atpA_p2 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC GGAACGTTTTCTACTTCAGGAG 378–404 1.000 53.6
trnR-AGA-atpA_p3 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC GGAACGTTTTCTACTTCAGGA 378–404 1.000 52.2
trnR-AGA-atpA_p4 trnR-AGA-atpA GCGAAAAGCGTCCATTGTCT GGAACGTTTTCTACTTCAGGAGA 378–404 1.000 50.9
trnR-AGA-atpA_p5 trnR-AGA-atpA GCGAAAAGCGTCCATTGTCT GGAACGTTTTCTACTTCAGGAG 378–404 1.000 49.8
petN-psbM_p1 petN-psbM TCGTAGTGTGGGGAAGAAGT GCACTCTTCATTCTCGTTCCT 642–644 1.000 76.4
petN-psbM_p2 petN-psbM CGTAGTGTGGGGAAGAAGTG GCACTCTTCATTCTCGTTCCT 641–643 1.000 75.8
petN-psbM_p3 petN-psbM TCGTAGTGTGGGGAAGAAGT ACTGCACTCTTCATTCTCGT 645–647 1.000 75.7
petN-psbM_p4 petN-psbM CGTAGTGTGGGGAAGAAGTG ACTGCACTCTTCATTCTCGT 644–646 1.000 75.1
petN-psbM_p5 petN-psbM CTCTCGTAGTGTGGGGAAGA GCACTCTTCATTCTCGTTCCT 645–647 1.000 75.1

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
Aphragmus involucratus NC_049579.1 153077 View on NCBI ↗
Aphragmus nepalensis NC_049584.1 149346 View on NCBI ↗