Markers + reference

Camelina

7 species · Brassicaceae · Brassicales

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Species 7
Genome length 153–154 kb
Candidate markers 264
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-trnC-GCA LSC 1111 0.0092 0.99 55.3 yes View details
trnL-UAA-trnF-GAA LSC 1315 0.0327 0.53 60.2 yes View details
trnP-UGG-psaJ LSC 385 0.0112 0.98 42.1 yes View details
psaJ-rpl33 LSC 436 0.0148 1.00 57.2 yes View details
rpl36-rps8 LSC 464 0.0094 1.00 48.6 yes View details
ycf1 IRb 1023 0.0003 1.00 42.9 no View details
rpl32-trnL-UAG SSC 669 0.0101 1.00 50.1 yes View details
ycf1 SSC 5397 0.0045 1.00 48.1 yes View details
atpB-rbcL LSC 799 0.0049 1.00 58.4 yes View details
petD-rpoA LSC 206 0.0132 1.00 57.2 yes View details
trnT-GGU-psbD LSC 1029 0.0044 1.00 56.7 yes View details
trnH-GUG-psbA LSC 278 0.0140 1.00 56.5 yes View details
psbM-trnD-GUC LSC 1013 0.0044 1.00 56.1 yes View details
psbE-petL LSC 1381 0.0031 0.99 56.1 yes View details
trnK-UUU-trnQ-UUG LSC 1141 0.0062 1.00 55.9 yes View details
trnS-GCU-trnG-UCC LSC 640 0.0034 1.00 54.6 yes View details
petN-psbM LSC 535 0.0043 1.00 53.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 336–342 1.000 82.3
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 337–343 1.000 82.1
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 351–357 1.000 82.0
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 354–360 1.000 81.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 352–358 1.000 81.8
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG CTACCGCAGATTTGGACGAA GAGGTTCGAATCCTTCCGTC 1263–1836 1.000 81.3
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 1199–1772 1.000 80.1
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 1198–1771 1.000 80.1
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG CGCAGATTTGGACGAATCCT GAGGTTCGAATCCTTCCGTC 1259–1832 1.000 78.6
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG CTCTACCGCAGATTTGGACG GAGGTTCGAATCCTTCCGTC 1265–1838 1.000 77.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCAACGCTTTAGTCCACTCA TGAATCAAACCGAGAGACCC 747–755 1.000 73.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AACGCTTTAGTCCACTCAGC TGAATCAAACCGAGAGACCC 745–753 1.000 73.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAGAGACCC 742–750 1.000 71.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCCAACGCTTTAGTCCACTC TGAATCAAACCGAGAGACCC 748–756 1.000 71.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CCAACGCTTTAGTCCACTCA GAATCAAACCGAGAGACCCT 746–754 1.000 71.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCGGGTATTGTAGATGTTCCC CCGGATTTGAACTGGGGAAA 841–1214 1.000 76.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCCCTCTTTTTCATCCCCA CCGGATTTGAACTGGGGAAA 826–1199 1.000 75.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TGTTCCCTCTTTTTCATCCCC CCGGATTTGAACTGGGGAAA 827–1200 1.000 75.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCTCTTTTTCATCCCCAAGC CCGGATTTGAACTGGGGAAA 822–1195 1.000 74.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGGGTATTGTAGATGTTCCC AAAAGGATTTGCAGTCCCCC 823–1196 1.000 73.8
petN-psbM_p1 petN-psbM TCGTAGTGTGGGGAAGAAGT GCACTCTTCATTCTCGTTCCT 636–640 1.000 72.7
petN-psbM_p2 petN-psbM CGTAGTGTGGGGAAGAAGTG GCACTCTTCATTCTCGTTCCT 635–639 1.000 72.1
petN-psbM_p3 petN-psbM GGGGCAGAATTCACATGGAT GCACTCTTCATTCTCGTTCCT 711–715 1.000 72.0
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT ACTGCACTCTTCATTCTCGT 639–643 1.000 72.0
petN-psbM_p5 petN-psbM GGGGCAGAATTCACATGGAT ACTGCACTCTTCATTCTCGT 714–718 1.000 71.3
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 1112–1136 1.000 70.5
psbM-trnD-GUC_p2 psbM-trnD-GUC ACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 1108–1132 1.000 69.8
psbM-trnD-GUC_p3 psbM-trnD-GUC GGAACGAGAATGAAGAGTGCA TTCAATTGGTCAGAGCACCG 1111–1135 1.000 68.2
psbM-trnD-GUC_p4 psbM-trnD-GUC AACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 1109–1133 1.000 67.6
psbM-trnD-GUC_p5 psbM-trnD-GUC GGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 1111–1135 1.000 67.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Camelina anomala NC_061686.1 154007 View on NCBI ↗
Camelina hispida NC_060480.1 153933 View on NCBI ↗
Camelina laxa NC_060478.1 154427 View on NCBI ↗
Camelina microcarpa NC_060477.1 153079 View on NCBI ↗
Camelina neglecta NC_060481.1 153481 View on NCBI ↗
Camelina rumelica NC_060479.1 152986 View on NCBI ↗
Camelina sativa NC_029337.1 153044 View on NCBI ↗