Markers + reference

Farsetia

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 155–155 kb
Candidate markers 270
Primer pairs 110

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 286 0.0427 0.98 78.7 yes View details
psbA LSC 1062 0.0028 1.00 50.2 yes View details
rps16-trnQ-CAA LSC 479 0.0189 0.99 67.7 yes View details
trnS-AGC-trnG-GGA LSC 688 0.0135 0.97 62.7 yes View details
psbM-trnD-GAC LSC 1020 0.0099 1.00 61.4 yes View details
trnT-ACC-psbD LSC 1051 0.0088 0.98 56.0 yes View details
psbC-trnS-UCA LSC 180 0.0294 0.94 60.9 yes View details
rbcL-accD LSC 713 0.0085 0.99 49.5 yes View details
rps8-rpl14 LSC 255 0.0196 1.00 55.3 yes View details
ycf1 IRb 1041 0.0000 1.00 40.0 no View details
rpl32-trnL-CUA SSC 757 0.0225 1.00 58.9 yes View details
rps15 SSC 267 0.0112 1.00 44.9 yes View details
ycf1 SSC 5322 0.0094 1.00 49.4 yes View details
petN-psbM LSC 544 0.0130 0.99 66.1 yes View details
trnT-ACA-trnL-UUA LSC 809 0.0051 0.97 64.7 yes View details
ndhJ-psbG LSC 101 0.0198 1.00 63.9 yes View details
petA-psbJ LSC 999 0.0090 1.00 63.9 yes View details
rpoC2-rpoC1 LSC 216 0.0165 0.84 63.5 yes View details
psbE-petL LSC 1397 0.0072 1.00 63.2 yes View details
trnK-AAA-rps16 LSC 633 0.0099 0.96 62.9 yes View details
rpl20-rps12 LSC 764 0.0065 1.00 62.5 yes View details
rpoB-trnC-UGC LSC 1155 0.0093 0.93 62.4 yes View details
psaA-ycf3 LSC 737 0.0041 0.99 62.3 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 110 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 TGTTGAGGCTCCATCTACCA 337–342 1.000 82.5
trnH-CAC-psbA_p2 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 339–344 1.000 82.5
trnH-CAC-psbA_p3 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC TGTTGAGGCTCCATCTACCA 338–343 1.000 82.3
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 354–359 1.000 82.2
trnH-CAC-psbA_p5 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 357–362 1.000 82.1
psbA_p1 psbA ACTAGGTCTAGACTAACGCT ATTTGTGTGCTTGGGAGTCC 1138 1.000 48.6
psbA_p2 psbA AACTAGGTCTAGACTAACGCT ATTTGTGTGCTTGGGAGTCC 1139 1.000 47.4
psbA_p3 psbA AGAAGGCTTATATTGCTCGT ATTTGTGTGCTTGGGAGTCC 1174 1.000 47.1
psbA_p4 psbA AAGAAGGCTTATATTGCTCGT ATTTGTGTGCTTGGGAGTCC 1175 1.000 45.9
psbA_p5 psbA AGAAGGCTTATATTGCTCGTT ATTTGTGTGCTTGGGAGTCC 1174 1.000 45.9
trnK-AAA-rps16_p1 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT AGGCAGGGATTTTTACGGAA 717–741 1.000 75.3
trnK-AAA-rps16_p2 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT AAGGCAGGGATTTTTACGGA 717–741 1.000 75.3
trnK-AAA-rps16_p3 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT AGGCAGGGATTTTTACGGAA 716–740 1.000 75.3
trnK-AAA-rps16_p4 trnK-AAA-rps16 AACTCTACCGCAGATCTGGA AAGGCAGGGATTTTTACGGA 786–810 1.000 75.1
trnK-AAA-rps16_p5 trnK-AAA-rps16 AACTCTACCGCAGATCTGGA AGGCAGGGATTTTTACGGAA 785–809 1.000 75.1
rps16-trnQ-CAA_p1 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 552–560 1.000 80.0
rps16-trnQ-CAA_p2 rps16-trnQ-CAA CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 562–570 1.000 79.2
rps16-trnQ-CAA_p3 rps16-trnQ-CAA CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 578 0.500 56.1
rps16-trnQ-CAA_p4 rps16-trnQ-CAA TCCACAGCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 579 0.500 56.0
rps16-trnQ-CAA_p5 rps16-trnQ-CAA ATCCACAGCAGATCATGTCC GAGGTTCGAATCCTTCCGTC 580 0.500 54.3
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTT 781–796 1.000 69.2
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA ATCAAACCGAGAGACCCTTT 780–795 1.000 69.2
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC AATCAAACCGAGAGACCCTT 779–794 1.000 68.9
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC ATCAAACCGAGAGACCCTTT 778–793 1.000 68.9
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTTT 781–796 1.000 67.3
rpoC2-rpoC1_p1 rpoC2-rpoC1 TGAAATACCAGATTGGCCCG ATCGAGAAATCGAGGAAGCT 270–304 1.000 72.0
rpoC2-rpoC1_p2 rpoC2-rpoC1 AATACCAGATTGGCCCGTTC ATCGAGAAATCGAGGAAGCT 267–301 1.000 72.0
rpoC2-rpoC1_p3 rpoC2-rpoC1 GAAATACCAGATTGGCCCGT ATCGAGAAATCGAGGAAGCT 269–303 1.000 72.0
rpoC2-rpoC1_p4 rpoC2-rpoC1 TGCCATCCCGAAGTGATCTA ATCGAGAAATCGAGGAAGCT 340–374 1.000 70.5
rpoC2-rpoC1_p5 rpoC2-rpoC1 AAATACCAGATTGGCCCGTT ATCGAGAAATCGAGGAAGCT 268–302 1.000 68.2

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
Farsetia occidentalis MK637823.1 154791 View on NCBI ↗
Farsetia stylosa NC_062802.1 154802 View on NCBI ↗