Markers + reference

Noccaea

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 153–153 kb
Candidate markers 270
Primer pairs 100

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-AAA-rps16 LSC 669 0.0183 0.98 58.7 yes View details
rps16 LSC 1164 0.0138 1.00 52.4 yes View details
rps16-trnQ-CAA LSC 450 0.0205 0.97 55.9 yes View details
psbM-trnD-GAC LSC 1039 0.0164 1.00 63.0 yes View details
rbcL-accD LSC 701 0.0158 0.99 60.1 yes View details
rpl33-rps18 LSC 208 0.0539 0.98 83.5 yes View details
rps18 LSC 306 0.0033 1.00 40.6 yes View details
ycf1 IRb 1035 0.0010 1.00 58.5 no View details
rpl32-trnL-CUA SSC 991 0.0205 0.94 67.5 yes View details
ccsA SSC 987 0.0152 1.00 59.2 yes View details
ndhE SSC 306 0.0065 1.00 41.9 yes View details
ycf1 SSC 5328 0.0094 1.00 48.2 yes View details
trnM-AUG-atpE LSC 140 0.0432 0.99 77.1 yes View details
trnG-GGA-trnR-AGA LSC 168 0.0539 0.99 69.0 yes View details
psbZ-trnG-GGC LSC 507 0.0179 0.99 67.8 yes View details
trnH-CAC-psbA LSC 314 0.0198 0.80 64.4 yes View details
rps11-rpl36 LSC 95 0.0213 0.99 64.4 yes View details
psaC-ndhE SSC 243 0.0247 1.00 64.4 yes View details
psbK-psbI LSC 403 0.0199 1.00 64.1 yes View details
psbG-ndhC LSC 59 0.0172 0.98 64.0 yes View details
rpl2-trnH-CAC IRa 56 0.0000 1.00 63.9 no 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 100 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 310–372 1.000 83.7
trnH-CAC-psbA_p2 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 325–387 1.000 83.5
trnH-CAC-psbA_p3 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 311–373 1.000 83.5
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 328–390 1.000 83.4
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 326–388 1.000 83.3
trnK-AAA-rps16_p1 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT CGGAATTAAGTCTTAATAAAACGA 732–738 1.000 42.7
trnK-AAA-rps16_p2 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT CGGAATTAAGTCTTAATAAAACGA 731–737 1.000 42.7
trnK-AAA-rps16_p3 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT CGGAATTAAGTCTTAATAAAACGAA 731–737 1.000 42.7
trnK-AAA-rps16_p4 trnK-AAA-rps16 AACTCTACCGCAGATCTGGA CGGAATTAAGTCTTAATAAAACGA 800–806 1.000 42.5
trnK-AAA-rps16_p5 trnK-AAA-rps16 AACTCTACCGCAGATCTGGA CGGAATTAAGTCTTAATAAAACGAA 800–806 1.000 42.5
rps16_p1 rps16 CATGTGTGCGTCAGGGATAA GAGGTTCGAATCCTTCCGTC 2232–2246 1.000 81.6
rps16_p2 rps16 AAATCCAGTCATGTGTGCGT GAGGTTCGAATCCTTCCGTC 2241–2255 1.000 80.9
rps16_p3 rps16 CATGTGTGCGTCAGGGATAA CTTCTATTGCCTTTGCGCAC 2199 0.500 59.0
rps16_p4 rps16 CATGTGTGCGTCAGGGATAA CGCACCACCTTTCTCTTTCT 2184 0.500 58.9
rps16_p5 rps16 CATGTGTGCGTCAGGGATAA TCTTCTATTGCCTTTGCGCA 2200 0.500 58.4
rps16-trnQ-CAA_p1 rps16-trnQ-CAA AAACGCTTGATTCACGCATG GAGGTTCGAATCCTTCCGTC 885–889 1.000 81.8
rps16-trnQ-CAA_p2 rps16-trnQ-CAA CAAACGCTTGATTCACGCAT GAGGTTCGAATCCTTCCGTC 886–890 1.000 81.8
rps16-trnQ-CAA_p3 rps16-trnQ-CAA AAACGCTTGATTCACGCATG CTTACAGCTGCTTGCCAAAC 1449–1453 1.000 81.1
rps16-trnQ-CAA_p4 rps16-trnQ-CAA CAAACGCTTGATTCACGCAT CTTACAGCTGCTTGCCAAAC 1450–1454 1.000 81.1
rps16-trnQ-CAA_p5 rps16-trnQ-CAA TTGATTCGCACTAACCCTGG CTTACAGCTGCTTGCCAAAC 1299 0.500 58.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCAGCTGTAAG TTTTATTCTTCGCGTCCCGG 546–548 1.000 75.8
psbK-psbI_p2 psbK-psbI TGGCAAGCAGCTGTAAGTTT TTTTATTCTTCGCGTCCCGG 543–545 1.000 73.7
psbK-psbI_p3 psbK-psbI TTGGCAAGCAGCTGTAAGTT TTTTATTCTTCGCGTCCCGG 544–546 1.000 73.7
psbK-psbI_p4 psbK-psbI TTTGGCAAGCAGCTGTAAGT TTTTATTCTTCGCGTCCCGG 545–547 1.000 73.7
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG CCGGATTACGTCCTGGATCA 530–532 1.000 73.2
trnG-GGA_p1 trnG-GGA GAATCCCGCGCTAGAATTTG AAAAAGGGGCAATTTAGGAT 929 0.500 20.0
trnG-GGA_p2 trnG-GGA GAATCCCGCGCTAGAATTTG AAAAGGGGCAATTTAGGATT 928 0.500 20.0
trnG-GGA_p3 trnG-GGA GAATCCCGCGCTAGAATTTG AAAGGGGCAATTTAGGATTT 927 0.500 20.0
trnG-GGA_p4 trnG-GGA GAATCCCGCGCTAGAATTTG AAAAAGGGGCAATTTAGGATT 929 0.500 20.0
trnG-GGA_p5 trnG-GGA GAATCCCGCGCTAGAATTTG AAAAGGGGCAATTTAGGATTT 928 0.500 20.0

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
Noccaea caerulescens NC_049682.1 152990 View on NCBI ↗
Noccaea vesicaria NC_049684.1 152694 View on NCBI ↗