Markers + reference

Arabidopsis

24 species · Brassicaceae · Brassicales

Back to catalogue

Species 24
Genome length 154–155 kb
Candidate markers 277
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-matK LSC 303 0.0078 1.00 45.9 yes View details
trnK-rps16 LSC 686 0.0121 1.00 59.3 yes View details
trnS-trnG LSC 654 0.0183 1.00 75.0 yes View details
rpoB-trnC LSC 1098 0.0094 1.00 63.5 yes View details
trnE-trnT LSC 831 0.0098 0.99 67.1 yes View details
trnL-trnF LSC 488 0.0166 0.92 62.0 yes View details
rbcL-accD LSC 682 0.0098 0.99 63.4 yes View details
psbE-ORF31 LSC 1382 0.0089 1.00 63.5 yes View details
psaJ-rpl33 LSC 437 0.0124 0.99 57.3 yes View details
ycf1 IRb 1032 0.0015 1.00 38.7 no View details
ndhF-rpl32 SSC 852 0.0170 0.99 73.2 yes View details
rpl32-trnL SSC 742 0.0118 1.00 70.9 yes View details
ycf1 SSC 5361 0.0059 1.00 59.6 yes View details
trnH-psbA LSC 280 0.0157 0.99 71.5 yes View details
atpB-rbcL LSC 809 0.0065 1.00 66.5 yes View details
clpP-clpP LSC 562 0.0073 1.00 66.0 yes View details
psbA-trnK LSC 268 0.0148 1.00 64.5 yes View details
ycf9-trnG LSC 495 0.0094 1.00 62.5 yes View details
trnT-trnL LSC 701 0.0058 1.00 62.2 yes View details
petA-psbJ LSC 1017 0.0056 1.00 61.9 yes View details
psbG-ndhC LSC 61 0.0143 1.00 61.3 yes View details
clpP-clpP LSC 885 0.0067 1.00 60.7 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 328–381 1.000 89.8
trnH-psbA_p2 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 329–382 1.000 89.5
trnH-psbA_p3 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 343–396 1.000 89.4
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 346–399 1.000 89.2
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 344–397 1.000 89.1
psbA-trnK_p1 psbA-trnK TACAGAAGCGACCCCATAGG AAAATGCAAGCACGGTTTGG 431–451 1.000 79.1
psbA-trnK_p2 psbA-trnK ATCCAGTTACAGAAGCGACC AAAATGCAAGCACGGTTTGG 438–458 1.000 78.3
psbA-trnK_p3 psbA-trnK ACGGTTTTCAGTGCTGGTTA AAAATGCAAGCACGGTTTGG 457–477 0.917 74.8
psbA-trnK_p4 psbA-trnK ACGGTTTTCAGTGCTGGTTA ACTCCATCCGACTAGTTCCG 389–411 0.917 73.8
psbA-trnK_p5 psbA-trnK ACGGTTTTCAGTGCTGGTTA TGAAAAATGCAAGCACGGTT 460–480 0.917 73.4
trnK-matK_p1 trnK-matK ACTCGAACCCGGAACTAGTC TCGAGTGCGAATTTGGTATTTG 386–393 1.000 59.2
trnK-matK_p2 trnK-matK GACTCGAACCCGGAACTAGT TCGAGTGCGAATTTGGTATTTG 387–394 1.000 59.2
trnK-matK_p3 trnK-matK ACTCGAACCCGGAACTAGTC TCGAGTGCGAATTTGGTATT 386–393 1.000 57.7
trnK-matK_p4 trnK-matK TACGATCCATAGTGGGTTGC TCGAGTGCGAATTTGGTATTTG 411–418 0.958 57.3
trnK-matK_p5 trnK-matK CGATCCATAGTGGGTTGCC TCGAGTGCGAATTTGGTATTTG 409–416 0.958 56.5
trnK-rps16_p1 trnK-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1027–1071 0.917 83.4
trnK-rps16_p2 trnK-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 1028–1072 0.917 83.4
trnK-rps16_p3 trnK-rps16 TCAGGATCAGTCGTGGTCTT CCCAATGAGCCGTTTATCGA 1023–1067 0.917 83.0
trnK-rps16_p4 trnK-rps16 TCAGGATCAGTCGTGGTCTT TCCCAATGAGCCGTTTATCG 1024–1068 0.917 83.0
trnK-rps16_p5 trnK-rps16 TTCAGGATCAGTCGTGGTCT CCCAATGAGCCGTTTATCGA 1024–1068 0.917 83.0
trnS-trnG_p1 trnS-trnG CCAACGCTTTAGTCCACTCA AACCGAGAGACCCTTTAACT 692–878 1.000 71.7
trnS-trnG_p2 trnS-trnG AACGCTTTAGTCCACTCAGC AACCGAGAGACCCTTTAACT 690–876 1.000 71.4
trnS-trnG_p3 trnS-trnG GAGAAGGGGAAAGAGAGGGA AACCGAGAGACCCTTTAACT 755–941 1.000 70.7
trnS-trnG_p4 trnS-trnG AGGAGAAGGGGAAAGAGAGG AACCGAGAGACCCTTTAACT 757–943 1.000 70.6
trnS-trnG_p5 trnS-trnG CCAACGCTTTAGTCCACTCA AAACCGAGAGACCCTTTAACT 693–879 1.000 70.0
rpoB-trnC_p1 rpoB-trnC CCGGGTATTGTAGATGTTCCC CCGGATTTGAACTGGGGAAA 1146–1216 1.000 79.2
rpoB-trnC_p2 rpoB-trnC GTTCCCTCTTTTTCATCCCCA CCGGATTTGAACTGGGGAAA 1131–1201 1.000 78.8
rpoB-trnC_p3 rpoB-trnC TGTTCCCTCTTTTTCATCCCC CCGGATTTGAACTGGGGAAA 1132–1202 1.000 78.8
rpoB-trnC_p4 rpoB-trnC CCTCTTTTTCATCCCCAAGC CCGGATTTGAACTGGGGAAA 1127–1197 1.000 77.5
rpoB-trnC_p5 rpoB-trnC CCGGGTATTGTAGATGTTCCC AAAAGGATTTGCAGTCCCCC 1128–1198 1.000 77.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (24)

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

Species Accession Length (bp) Link
Arabidopsis arenicola NC_030346.1 154610 View on NCBI ↗
Arabidopsis arenosa NC_029334.1 154871 View on NCBI ↗
Arabidopsis cebennensis NC_029335.1 154504 View on NCBI ↗
Arabidopsis croatica NC_030347.1 154728 View on NCBI ↗
Arabidopsis halleri NC_034366.1 154671 View on NCBI ↗
Arabidopsis halleri subsp. dacica LT161929.1 154813 View on NCBI ↗
Arabidopsis halleri subsp. gemmifera KU764767.1 154473 View on NCBI ↗
Arabidopsis halleri subsp. halleri LT161932.1 154829 View on NCBI ↗
Arabidopsis halleri subsp. ovirensis LT161934.1 154919 View on NCBI ↗
Arabidopsis halleri subsp. tatrica LT161936.1 154884 View on NCBI ↗
Arabidopsis kamchatica subsp. kamchatica LT161938.1 154618 View on NCBI ↗
Arabidopsis kamchatica subsp. kawasakiana LT161941.1 154339 View on NCBI ↗
Arabidopsis lyrata NC_034365.1 154678 View on NCBI ↗
Arabidopsis lyrata subsp. lyrata NC_034379.1 154923 View on NCBI ↗
Arabidopsis lyrata subsp. petraea KU764768.1 154489 View on NCBI ↗
Arabidopsis neglecta NC_030348.1 154799 View on NCBI ↗
Arabidopsis neglecta subsp. neglecta LT161964.1 154911 View on NCBI ↗
Arabidopsis pedemontana NC_029336.1 154895 View on NCBI ↗
[Arabidopsis petraea] subsp. umbrosa LT161977.1 154573 View on NCBI ↗
Arabidopsis petrogena NC_030349.1 154865 View on NCBI ↗
Arabidopsis septentrionalis LT161975.1 154873 View on NCBI ↗
Arabidopsis suecica NC_030350.1 154366 View on NCBI ↗
Arabidopsis thaliana NC_000932.1 154478 View on NCBI ↗
Arabidopsis umezawana NC_030351.1 154645 View on NCBI ↗