Markers + reference

Gnaphalium

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–153 kb
Candidate markers 271
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 8 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 363 0.0977 0.96 92.0 yes View details
trnK-UUU-rps16 LSC 816 0.0488 0.95 90.5 yes View details
trnS-GCU-trnC-GCA LSC 719 0.0669 0.96 82.2 yes View details
petN-psbM LSC 535 0.0566 0.96 77.2 yes View details
trnG-UCC-trnT-GGU LSC 385 0.1004 0.70 74.2 yes View details
trnT-GGU-psbD LSC 1342 0.0336 0.93 75.4 yes View details
psbZ-trnG-GCC LSC 324 0.0334 0.92 66.3 yes View details
trnG-GCC-trnfM-CAU LSC 243 0.0894 0.97 79.9 yes View details
trnT-UGU-trnL-UAA LSC 613 0.0505 0.91 82.2 yes View details
ycf1-rps15 SSC 404 0.0678 0.91 78.4 yes View details
trnL-UAG-rpl32 SSC 829 0.0842 0.85 77.4 yes View details
rpl32-ndhF SSC 1123 0.0541 0.89 78.2 yes View details
petA-psbJ LSC 801 0.0395 0.95 75.6 yes View details
psaB-psaA LSC 25 0.0400 1.00 75.5 yes View details
ycf4-cemA LSC 461 0.0535 0.93 75.3 yes View details
trnY-GUA-trnE-UUC LSC 183 0.0393 0.97 74.8 yes View details
psbC-trnS-UGA LSC 230 0.0405 0.97 74.7 yes View details
ycf3-trnS-GGA LSC 971 0.0265 0.97 74.6 yes View details
ndhC-trnV-UAC LSC 1197 0.0262 0.96 74.4 yes View details
ndhD-ccsA SSC 277 0.0642 0.96 74.3 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 482–499 1.000 84.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 496–513 1.000 84.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 495–512 1.000 84.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 497–514 1.000 84.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 483–500 1.000 83.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1004–1013 1.000 82.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 1003–1012 1.000 82.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 943–952 1.000 82.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 942–951 1.000 82.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1028–1037 1.000 81.5
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 787–806 1.000 82.0
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 769–788 1.000 80.0
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA TTTCGTCCACTCAGCCATCT CCGGATTTGAACTGGGGAAA 786–805 1.000 78.9
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA TCCACTCAGCCATCTCTCC CCGGATTTGAACTGGGGAAA 781–800 1.000 78.4
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA ATTAGCAATCCGCCGCTTT CCGGATTTGAACTGGGGAAA 802–821 1.000 77.3
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT GGAGGGACAGAGAGCAATTG 1324–1338 1.000 83.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT AAGGAGGGACAGAGAGCAAT 1326–1340 1.000 83.2
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT AGGAGGGACAGAGAGCAATT 1325–1339 1.000 83.2
petN-psbM_p4 petN-psbM TCGGGAAAGGGTACGGATTA GGAGGGACAGAGAGCAATTG 1695 0.500 58.5
petN-psbM_p5 petN-psbM TCGGGAAAGGGTACGGATTA AGGAGGGACAGAGAGCAATT 1696 0.500 58.5
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC AAAACGAGGGTTCAAGTCCC 251–256 1.000 80.8
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC ACGAATTTACAGTCCGTCCC AAAACGAGGGTTCAAGTCCC 252–257 1.000 80.6
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC CCCCTATGGTCCAGTGGTTA 292–297 1.000 79.6
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC GATGTATGATGGCCACAGGG 320 0.500 56.4
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC ACGAATTTACAGTCCGTCCC GATGTATGATGGCCACAGGG 321 0.500 56.2
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU AATCAAACCGAAAGACCCCT ATTTGAACCGAGGGCTTACG 393–503 1.000 78.9
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ATCAAACCGAAAGACCCCTT ATTTGAACCGAGGGCTTACG 392–502 1.000 78.9
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ATCAAACCGAAAGACCCCTT AGGGCTTACGCTTTACACTC 382–492 1.000 78.1
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ATCAAACCGAAAGACCCCTT GAGGGCTTACGCTTTACACT 383–493 1.000 78.1
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU ATCAAACCGAAAGACCCCTT GGGCTTACGCTTTACACTCT 381–491 1.000 78.1

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
Gnaphalium palustre OR771722.1 152808 View on NCBI ↗
Gnaphalium polycaulon NC_087962.1 151588 View on NCBI ↗