Markers + reference

Arabis

8 species · Brassicaceae · Brassicales

Back to catalogue

Species 8
Genome length 154–154 kb
Candidate markers 290
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 290 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 399 0.0188 0.99 77.2 yes View details
trnK-rps16 LSC 686 0.0137 1.00 51.8 yes View details
rps16 LSC 1100 0.0123 1.00 54.3 yes View details
psbZ-trnG LSC 507 0.0134 1.00 60.9 yes View details
rbcL-accD LSC 736 0.0095 0.99 51.1 yes View details
petA-psbJ LSC 973 0.0137 0.99 60.0 yes View details
trnP-psaJ LSC 364 0.0175 0.94 49.0 yes View details
psaJ-rpl33 LSC 396 0.0177 0.99 59.7 yes View details
ycf1 IRb 1023 0.0007 1.00 34.8 no View details
ndhF-rpl32 SSC 815 0.0156 0.99 54.6 yes View details
rpl32-trnL SSC 883 0.0094 1.00 49.9 yes View details
ycf1 SSC 5340 0.0064 1.00 46.6 yes View details
psbE-petL LSC 917 0.0079 1.00 60.7 yes View details
trnT-trnL LSC 844 0.0073 0.99 60.5 yes View details
ndhC-trnV LSC 711 0.0081 0.99 59.3 yes View details
trnT-psbD LSC 901 0.0085 1.00 58.7 yes View details
trnE-trnT LSC 439 0.0105 1.00 58.3 yes View details
trnS-trnG LSC 718 0.0099 1.00 57.8 yes View details
psaA-ycf3 LSC 729 0.0045 1.00 57.1 yes View details
atpB-rbcL LSC 828 0.0080 1.00 54.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 446–499 1.000 87.3
trnH-psbA_p2 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 461–514 1.000 87.0
trnH-psbA_p3 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 447–500 1.000 87.0
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 464–517 1.000 86.9
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 462–515 1.000 86.8
trnK-rps16_p1 trnK-rps16 CCTTTCAGGATCAGTCGTGG CCGTTTATCGAATCGTTGCG 985–999 1.000 85.8
trnK-rps16_p2 trnK-rps16 TCGACACCGAAAACAAGGTT CCGTTTATCGAATCGTTGCG 1078–1092 1.000 85.5
trnK-rps16_p3 trnK-rps16 TCAGGATCAGTCGTGGTCTT CCGTTTATCGAATCGTTGCG 981–995 1.000 85.3
trnK-rps16_p4 trnK-rps16 TTCAGGATCAGTCGTGGTCT CCGTTTATCGAATCGTTGCG 982–996 1.000 85.3
trnK-rps16_p5 trnK-rps16 CCTTTCAGGATCAGTCGTGG AGGCAAAAGCCTCGTATACG 1061 0.875 75.5
rps16_p1 rps16 CATGTGTGCGTCAGGGATAA GAGGTTCGAATCCTTCCGTC 2150–2171 1.000 84.9
rps16_p2 rps16 CATGTGTGCGTCAGGGATAA AAAAATCGACATGGGGCGTA 2209–2230 1.000 84.4
rps16_p3 rps16 CATGTGTGCGTCAGGGATAA TAAAAATCGACATGGGGCGT 2210–2231 1.000 84.4
rps16_p4 rps16 AAATCCAGTCATGTGTGCGT GAGGTTCGAATCCTTCCGTC 2159–2180 1.000 84.2
rps16_p5 rps16 AAATCCAGTCATGTGTGCGT AAAAATCGACATGGGGCGTA 2218–2239 1.000 83.7
trnS-trnG_p1 trnS-trnG CTTTAGTCCGCTCAGCCATC TACCACTAAACTACACCCGC 716–768 1.000 75.1
trnS-trnG_p2 trnS-trnG GCAATCCAACGCTTTAGTCC TACCACTAAACTACACCCGC 727–779 1.000 74.1
trnS-trnG_p3 trnS-trnG CTTTAGTCCGCTCAGCCATC TTACCACTAAACTACACCCGC 717–769 1.000 72.8
trnS-trnG_p4 trnS-trnG TTTAGTCCGCTCAGCCATCT TACCACTAAACTACACCCGC 715–767 1.000 72.0
trnS-trnG_p5 trnS-trnG CAATCCAACGCTTTAGTCCG TACCACTAAACTACACCCGC 726–778 1.000 72.0
trnE-trnT_p1 trnE-trnT TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 570–582 1.000 82.5
trnE-trnT_p2 trnE-trnT TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 549–561 1.000 82.2
trnE-trnT_p3 trnE-trnT TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 546–558 1.000 82.1
trnE-trnT_p4 trnE-trnT GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 532–544 1.000 82.0
trnE-trnT_p5 trnE-trnT TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 511–523 1.000 82.0
trnT-psbD_p1 trnT-psbD GTGGTAGAGTAACGCCATGG ACCTACAAAAACGAAGCGGT 1055–1242 1.000 83.4
trnT-psbD_p2 trnT-psbD TCAGTGGTAGAGTAACGCCA ACCTACAAAAACGAAGCGGT 1058–1245 1.000 83.2
trnT-psbD_p3 trnT-psbD GGCGTAAGTCATCGGTTCAA ACCTACAAAAACGAAGCGGT 1032–1219 1.000 81.7
trnT-psbD_p4 trnT-psbD TGGTAGAGTAACGCCATGGT ACCTACAAAAACGAAGCGGT 1054–1241 1.000 80.4
trnT-psbD_p5 trnT-psbD GTGGTAGAGTAACGCCATGG TCCCTCCGTAACCAGTCATC 1036–1223 1.000 79.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Arabis flagellosa NC_037475.1 153673 View on NCBI ↗
Arabis hirsuta NC_009268.1 153689 View on NCBI ↗
Arabis hirsuta var. nipponica LC361349.1 153668 View on NCBI ↗
Arabis paniculata NC_053754.1 153541 View on NCBI ↗
Arabis scabra NC_048493.1 153690 View on NCBI ↗
Arabis stelleri NC_068066.1 153572 View on NCBI ↗
Arabis stelleri subsp. japonica KY126841.1 153683 View on NCBI ↗
Arabis takesimana OR813051.1 153557 View on NCBI ↗