Markers + reference

Centaurea

11 species · Asteraceae · Asterales

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Species 11
Genome length 152–153 kb
Candidate markers 271
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 775 0.0081 1.00 45.0 yes View details
petN-psbM LSC 505 0.0103 1.00 44.3 yes View details
trnE-UUC-rpoB LSC 924 0.0070 0.99 48.5 yes View details
ycf3-trnS-GGA LSC 909 0.0114 1.00 47.7 yes View details
trnS-GGA-rps4 LSC 310 0.0082 1.00 39.2 yes View details
ycf1 IRb 588 0.0031 1.00 39.3 no View details
rpl32-trnL-UAG SSC 814 0.0100 1.00 41.1 yes View details
ndhG-ndhI SSC 373 0.0153 0.96 44.5 yes View details
rps15-ycf1 SSC 423 0.0100 0.98 48.7 yes View details
ycf1 SSC 5178 0.0069 1.00 36.5 yes View details
ndhC-trnV-UAC LSC 1152 0.0062 1.00 59.0 yes View details
petA-psbJ LSC 807 0.0064 0.99 55.6 yes View details
atpH-atpF LSC 367 0.0062 0.99 51.9 yes View details
atpI-atpH LSC 1143 0.0044 1.00 50.9 yes View details
ndhA SSC 2152 0.0049 1.00 50.1 yes View details
matK-trnK-UUU LSC 728 0.0038 1.00 48.3 yes View details
rpl20-rps12 LSC 745 0.0022 1.00 48.1 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU ACCATGATCATGAGCAAGTACA AACGGTAGAGTACTCGGCTT 860–867 1.000 59.6
matK-trnK-UUU_p2 matK-trnK-UUU ACCATGATCATGAGCAAGTACA ACGGTAGAGTACTCGGCTTT 859–866 1.000 59.6
matK-trnK-UUU_p3 matK-trnK-UUU ACCATGATCATGAGCAAGTACA TTGGGTTGCTAACTCAACGG 875–882 1.000 57.8
matK-trnK-UUU_p4 matK-trnK-UUU ACCATGATCATGAGCAAGTACA GGGTTGCTAACTCAACGGTA 873–880 1.000 57.3
matK-trnK-UUU_p5 matK-trnK-UUU AACCATGATCATGAGCAAGT ACGGTAGAGTACTCGGCTTT 860–867 1.000 55.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 973–1004 1.000 78.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 972–1003 1.000 78.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 912–943 1.000 78.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 911–942 1.000 78.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC ACTTTGCCCTAATCAAGCGA 901–932 1.000 77.4
petN-psbM_p1 petN-psbM GGGGAAGAAGTGGGCTTTAG ACGTAAAAACAGTCAGTCAA 554–560 1.000 42.7
petN-psbM_p2 petN-psbM GGGGAAGAAGTGGGCTTTAG ACGTAAAAACAGTCAGTCAAA 554–560 1.000 42.7
petN-psbM_p3 petN-psbM GGGGAAGAAGTGGGCTTTAG ACGTAAAAACAGTCAGTCAAAATGA 554–560 1.000 42.7
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTAAAAACAGTCAGTCAA 617–623 1.000 42.5
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTAAAAACAGTCAGTCAAA 617–623 1.000 42.5
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GAGAGAAGTCGTAACCGCTG TCTGATTAAATCCAGGTATTGTGG 939–985 1.000 46.1
trnE-UUC-rpoB_p2 trnE-UUC-rpoB GAGAGAAGTCGTAACCGCTG TCAATGAACCTACAAAATCCTTCA 970–1016 0.909 42.2
trnE-UUC-rpoB_p3 trnE-UUC-rpoB AACCCTCGTTATCTCCGTGA TCAATGAACCTACAAAATCCTTCA 992–1038 0.909 42.2
trnE-UUC-rpoB_p4 trnE-UUC-rpoB ACCCTCGTTATCTCCGTGAA TCAATGAACCTACAAAATCCTTCA 991–1037 0.909 42.2
trnE-UUC-rpoB_p5 trnE-UUC-rpoB TGAACCCTCGTTATCTCCGT TCAATGAACCTACAAAATCCTTCA 994–1040 0.909 42.2
atpI-atpH_p1 atpI-atpH TCCCTGTCATGTTCCTTGGA ATAACGGAAGCGGCAGAAAT 1265–1279 1.000 79.9
atpI-atpH_p2 atpI-atpH TCCCTGTCATGTTCCTTGGA TACCTTGACCAACTCCAGGT 1321–1335 1.000 79.3
atpI-atpH_p3 atpI-atpH TCCCTGTCATGTTCCTTGGA AGCCAATCCAGCAGCAATAA 1281–1295 1.000 79.0
atpI-atpH_p4 atpI-atpH TCCCTGTCATGTTCCTTGGA AATAACGGAAGCGGCAGAAA 1266–1280 1.000 78.8
atpI-atpH_p5 atpI-atpH TCCCTGTCATGTTCCTTGGA GCAGTACCTTGACCAACTCC 1325–1339 1.000 78.6
atpH-atpF_p1 atpH-atpF GCCTGGTTGTAGCATTAGCA TGGCCCAAAGAAACGAAAGA 440–479 1.000 81.4
atpH-atpF_p2 atpH-atpF GCCTGGTTGTAGCATTAGCA GTGGCCCAAAGAAACGAAAG 441–480 1.000 80.8
atpH-atpF_p3 atpH-atpF GCCTGGTTGTAGCATTAGCA ATTAAACCCGAAACTCCCGG 471–510 1.000 80.7
atpH-atpF_p4 atpH-atpF TGGCCTGGTTGTAGCATTAG TGGCCCAAAGAAACGAAAGA 442–481 1.000 80.1
atpH-atpF_p5 atpH-atpF GCCTGGTTGTAGCATTAGCA AGTGGCCCAAAGAAACGAAA 442–481 1.000 80.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Centaurea bracteata OR909615.1 152603 View on NCBI ↗
Centaurea diffusa NC_024286.1 152559 View on NCBI ↗
Centaurea jacea OR909628.1 152585 View on NCBI ↗
Centaurea jacea subsp. julica OR909629.1 152600 View on NCBI ↗
Centaurea maculosa MN228501.1 152518 View on NCBI ↗
Centaurea nigrescens subsp. nigrescens OR909616.1 152617 View on NCBI ↗
Centaurea scabiosa subsp. alpestris OR909630.1 152698 View on NCBI ↗
Centaurea scabiosa subsp. grinensis OR909631.1 152701 View on NCBI ↗
Centaurea scabiosa subsp. scabiosa OR909632.1 152700 View on NCBI ↗
Centaurea stoebe OR909617.1 152533 View on NCBI ↗
Centaurea triumfettii OR909618.1 152234 View on NCBI ↗