Markers + reference

Orychophragmus

6 species · Brassicaceae · Brassicales

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Species 6
Genome length 153–154 kb
Candidate markers 256
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 256 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 281 0.0269 0.68 58.3 yes View details
trnS-trnG LSC 666 0.0206 0.96 74.0 yes View details
trnC-petN LSC 603 0.0143 1.00 52.4 yes View details
trnE-trnT LSC 660 0.0091 0.99 59.1 yes View details
BZJ73_gt016-trnL LSC 806 0.0121 1.00 59.4 yes View details
ndhC-trnV LSC 882 0.0112 0.96 63.0 yes View details
petA-psbJ LSC 951 0.0147 0.99 59.8 yes View details
psbE-petL LSC 940 0.0094 1.00 55.7 yes View details
ycf1 IRb 1041 0.0005 1.00 38.4 no View details
ndhF-rpl32 SSC 854 0.0193 0.98 64.4 yes View details
rpl32-trnL SSC 690 0.0171 0.88 59.1 yes View details
ycf1 SSC 5328 0.0070 1.00 43.7 yes View details
psaA-ycf3 LSC 698 0.0077 1.00 65.2 yes View details
psbM-trnD LSC 1027 0.0080 0.99 60.2 yes View details
rpl36-rps8 LSC 480 0.0148 0.99 60.0 yes View details
psbZ-trnG LSC 460 0.0097 0.98 58.3 yes View details
trnN-trnR IRa 616 0.0040 1.00 57.3 yes View details
rpl20-rps12 LSC 783 0.0051 0.98 57.1 yes View details
trnR-trnN IRb 616 0.0035 1.00 56.9 yes View details
rbcL-accD LSC 680 0.0085 0.99 54.7 yes View details
ccsA SSC 987 0.0049 1.00 54.7 yes View details
rps16-trnQ LSC 448 0.0081 0.98 54.5 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 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 248–362 1.000 85.9
trnH-psbA_p2 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 249–363 1.000 85.7
trnH-psbA_p3 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 263–377 1.000 85.6
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 266–380 1.000 85.5
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 264–378 1.000 85.4
rps16-trnQ_p1 rps16-trnQ AAGGTGGCGGATCAAAACAT GAGGTTCGAATCCTTCCGTC 555–579 1.000 82.0
rps16-trnQ_p2 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 509–533 1.000 81.8
rps16-trnQ_p3 rps16-trnQ CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 519–543 1.000 81.0
rps16-trnQ_p4 rps16-trnQ AAAGGTGGCGGATCAAAACA GAGGTTCGAATCCTTCCGTC 556–580 1.000 80.2
rps16-trnQ_p5 rps16-trnQ AGGTGGCGGATCAAAACATC GAGGTTCGAATCCTTCCGTC 554–578 1.000 78.4
trnS-trnG_p1 trnS-trnG ACGCTTTAATCCACTCAGCC AATCAAACCGAGAGACCCTT 761–788 1.000 72.9
trnS-trnG_p2 trnS-trnG ACGCTTTAATCCACTCAGCC ATCAAACCGAGAGACCCTTT 760–787 1.000 72.9
trnS-trnG_p3 trnS-trnG CGCTTTAATCCACTCAGCCA AATCAAACCGAGAGACCCTT 760–787 1.000 72.9
trnS-trnG_p4 trnS-trnG CGCTTTAATCCACTCAGCCA ATCAAACCGAGAGACCCTTT 759–786 1.000 72.9
trnS-trnG_p5 trnS-trnG CGGAAGGGAAAGAGAGGGAT ATCAAACCGAGAGACCCTTT 825–852 1.000 70.6
trnC-petN_p1 trnC-petN TTTCCCCAGTTCAAATCCGG AGCCCATGCGAGACTTACTA 659–690 1.000 80.9
trnC-petN_p2 trnC-petN GTTTCTATCGTTTTGGCGGC AGCCCATGCGAGACTTACTA 715–746 1.000 80.4
trnC-petN_p3 trnC-petN TTCTATCGTTTTGGCGGCAT AGCCCATGCGAGACTTACTA 713–744 1.000 79.3
trnC-petN_p4 trnC-petN GGGGGACTGCAAATCCTTTT AGCCCATGCGAGACTTACTA 677–708 1.000 78.6
trnC-petN_p5 trnC-petN TTTCCCCAGTTCAAATCCGG ATTAAACCAGCCCATGCGAG 667–698 1.000 77.8
psbM-trnD_p1 psbM-trnD AGGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 1129–1145 1.000 71.4
psbM-trnD_p2 psbM-trnD ACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 1125–1141 1.000 70.7
psbM-trnD_p3 psbM-trnD GGAACGAGAATGAAGAGTGCA TTCAATTGGTCAGAGCACCG 1128–1144 1.000 69.1
psbM-trnD_p4 psbM-trnD AACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 1126–1142 1.000 68.5
psbM-trnD_p5 psbM-trnD GGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 1128–1144 1.000 68.0
trnE-trnT_p1 trnE-trnT TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 797–807 1.000 81.2
trnE-trnT_p2 trnE-trnT TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 776–786 1.000 80.8
trnE-trnT_p3 trnE-trnT TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 773–783 1.000 80.6
trnE-trnT_p4 trnE-trnT GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 759–769 1.000 80.5
trnE-trnT_p5 trnE-trnT TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 738–748 1.000 80.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Orychophragmus diffusus NC_033498.1 153777 View on NCBI ↗
Orychophragmus hupehensis NC_033500.1 153184 View on NCBI ↗
Orychophragmus longisiliquus KX756549.1 153365 View on NCBI ↗
Orychophragmus taibaiensis NC_033499.1 153255 View on NCBI ↗
Orychophragmus violaceus NC_049687.1 153135 View on NCBI ↗
Orychophragmus zhongtiaoshanus KX756547.1 153440 View on NCBI ↗