Markers + reference

Anaphalis

47 species · Asteraceae · Asterales

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Species 47
Genome length 152–156 kb
Candidate markers 263
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 403 0.0335 0.97 67.5 yes View details
trnK-UUU-rps16 LSC 843 0.0146 0.97 78.5 yes View details
trnR-UCU-trnG-UCC LSC 289 0.0412 0.80 72.3 yes View details
trnG-UCC-trnT-GGU LSC 446 0.0364 0.61 65.5 yes View details
trnT-GGU-psbD LSC 1326 0.0134 0.94 57.9 yes View details
psbZ-trnG-UCC LSC 302 0.0061 1.00 36.9 yes View details
trnG-UCC-trnfM-CAU LSC 271 0.0255 0.97 67.9 yes View details
psaA-ycf3 LSC 787 0.0098 0.98 59.5 yes View details
ndhC-trnV-UAC LSC 1227 0.0118 0.98 70.6 yes View details
trnL-UAG-rpl32 SSC 806 0.0107 0.97 65.1 yes View details
rpl32-ndhF SSC 1098 0.0111 0.95 62.4 yes View details
ndhD-ccsA SSC 270 0.0133 1.00 65.9 yes View details
rpl22-rps19 LSC 102 0.0202 1.00 64.6 yes View details
ycf3-trnS-GGA LSC 932 0.0074 0.98 63.8 yes View details
trnF-GAA-ndhJ LSC 681 0.0105 0.88 60.8 yes View details
accD-psaI LSC 663 0.0050 0.98 60.0 yes View details
petN-psbM LSC 508 0.0074 0.98 57.9 yes View details
psbM-trnD-GUC LSC 660 0.0053 0.99 57.8 yes View details
rps11-rpl36 LSC 100 0.0088 1.00 57.2 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 95 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 AAGCTCCATCTACAAATGG 384–503 1.000 52.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AAGCTCCATCTACAAATGG 398–517 1.000 52.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AAGCTCCATCTACAAATGG 397–516 1.000 52.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AAGCTCCATCTACAAATGG 399–518 1.000 52.0
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC AAGCTCCATCTACAAATGG 413–532 1.000 52.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTGAAAAAGGTGCTCAGCCT 813–1110 1.000 88.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTGAAAAAGGTGCTCAGCCT 812–1109 1.000 88.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTGAAAAAGGTGCTCAGCCT 752–1049 1.000 88.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTGAAAAAGGTGCTCAGCCT 751–1048 1.000 88.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AAAAGGTGCTCAGCCTACAG 808–1105 1.000 87.8
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 663–700 1.000 63.9
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 663–700 1.000 62.2
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 664–701 1.000 58.0
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 655–692 1.000 58.0
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 649–686 1.000 57.2
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCTAGAGCACCG 758–795 1.000 51.9
psbM-trnD-GUC_p2 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCTAGAGCACCG 752–789 1.000 51.5
psbM-trnD-GUC_p3 psbM-trnD-GUC ACTAAAATGAACAGTGCAGTAGC TTCAATAGGCTAGAGCACCG 755–792 1.000 50.6
psbM-trnD-GUC_p4 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT CAATAGGCTAGAGCACCGC 756–793 1.000 50.3
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCAG TTCAATAGGCTAGAGCACCG 759–796 1.000 49.9
trnR-UCU-trnG-UCC_p1 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 307–369 1.000 75.3
trnR-UCU-trnG-UCC_p2 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 310–372 1.000 75.1
trnR-UCU-trnG-UCC_p3 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 313–375 1.000 74.7
trnR-UCU-trnG-UCC_p4 trnR-UCU-trnG-UCC AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 316–378 1.000 74.5
trnR-UCU-trnG-UCC_p5 trnR-UCU-trnG-UCC AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 311–373 1.000 72.9
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ATTTGAACCGAGGGCTTACG 523–579 0.362 29.3
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT AGGGCTTACGCTTTACACTC 513–569 0.362 28.4
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GAGGGCTTACGCTTTACACT 514–570 0.362 28.4
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GGGCTTACGCTTTACACTCT 512–568 0.362 28.4
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ATTTGAACCGAGGGCTTACG 525–581 0.362 28.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (47)

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

Species Accession Length (bp) Link
Anaphalis acutifolia NC_087913.1 153217 View on NCBI ↗
Anaphalis aureopunctata NC_087914.1 152622 View on NCBI ↗
Anaphalis aureopunctata var. plantaginifolia OR727197.1 152644 View on NCBI ↗
Anaphalis aurora NC_087915.1 153360 View on NCBI ↗
Anaphalis bicolor NC_087916.1 152607 View on NCBI ↗
Anaphalis brevifolia NC_087917.1 152719 View on NCBI ↗
Anaphalis bulleyana NC_087918.1 152767 View on NCBI ↗
Anaphalis busua NC_087919.1 153087 View on NCBI ↗
Anaphalis cavei NC_087920.1 153025 View on NCBI ↗
Anaphalis chlamydophylla NC_087921.1 152643 View on NCBI ↗
Anaphalis cinerascens NC_087922.1 152713 View on NCBI ↗
Anaphalis contorta NC_087923.1 153092 View on NCBI ↗
Anaphalis contortiformis NC_087924.1 152702 View on NCBI ↗
Anaphalis elegans NC_087926.1 152440 View on NCBI ↗
Anaphalis flaccida NC_087927.1 152679 View on NCBI ↗
Anaphalis flavescens NC_087928.1 152679 View on NCBI ↗
Anaphalis hancockii NC_087930.1 152662 View on NCBI ↗
Anaphalis hellwigii NC_087931.1 153229 View on NCBI ↗
Anaphalis hookeri PX910299.1 153209 View on NCBI ↗
Anaphalis hymenolepis NC_087932.1 152697 View on NCBI ↗
Anaphalis lactea NC_087933.1 152516 View on NCBI ↗
Anaphalis larium NC_087934.1 152667 View on NCBI ↗
Anaphalis likiangensis NC_087935.1 155752 View on NCBI ↗
Anaphalis margaritacea NC_087936.1 152832 View on NCBI ↗
Anaphalis margaritacea var. angustior OR727227.1 153269 View on NCBI ↗
Anaphalis muliensis NC_087937.1 152539 View on NCBI ↗
Anaphalis nepalensis NC_087938.1 153218 View on NCBI ↗
Anaphalis nubigena NC_087939.1 153122 View on NCBI ↗
Anaphalis pachylaena NC_087940.1 152454 View on NCBI ↗
Anaphalis racemifera NC_087942.1 153228 View on NCBI ↗
Anaphalis rhododactyla NC_087943.1 152726 View on NCBI ↗
Anaphalis roseoalba NC_087944.1 153359 View on NCBI ↗
Anaphalis royleana NC_087945.1 153930 View on NCBI ↗
Anaphalis sinica NC_034648.1 152718 View on NCBI ↗
Anaphalis souliei NC_087946.1 152706 View on NCBI ↗
Anaphalis stenocephala NC_087947.1 152781 View on NCBI ↗
Anaphalis subdecurrens NC_087948.1 153130 View on NCBI ↗
Anaphalis suffruticosa NC_087949.1 152571 View on NCBI ↗
Anaphalis surculosa NC_087950.1 152666 View on NCBI ↗
Anaphalis szechuanensis NC_087951.1 152826 View on NCBI ↗
Anaphalis tenella NC_087952.1 153145 View on NCBI ↗
Anaphalis tibetica NC_087953.1 153022 View on NCBI ↗
Anaphalis virens NC_087955.1 152837 View on NCBI ↗
Anaphalis virgata NC_087956.1 153361 View on NCBI ↗
Anaphalis viridis NC_087957.1 155770 View on NCBI ↗
Anaphalis xylorhiza NC_087958.1 152682 View on NCBI ↗
Anaphalis yunnanensis NC_087959.1 152646 View on NCBI ↗