Markers + reference

Mikania

16 species · Asteraceae · Asterales

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Species 16
Genome length 152–152 kb
Candidate markers 275
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 388 0.0215 1.00 65.0 yes View details
trnK-UUU-rps16 LSC 819 0.0102 0.99 60.0 yes View details
atpI-atpH LSC 1168 0.0093 1.00 71.0 yes View details
rbcL LSC 1458 0.0072 1.00 53.2 yes View details
rpl16 LSC 1426 0.0044 1.00 45.2 yes View details
rrn23 IRb 2812 0.0065 1.00 56.2 no View details
ycf1 SSC 5079 0.0066 1.00 52.0 yes View details
trnL-UAG-rpl32 SSC 744 0.0147 0.99 57.9 yes View details
rpl32-ndhF SSC 1008 0.0112 1.00 73.6 yes View details
ycf1 SSC 567 0.0019 1.00 42.7 no View details
rrn23 IRa 2812 0.0065 1.00 56.2 yes View details
rps19-trnH-GUG LSC 8 0.0781 1.00 81.7 no View details
ndhC-trnV-UAC LSC 1167 0.0069 0.98 71.3 yes View details
rpl36-infA LSC 115 0.0189 1.00 69.5 yes View details
atpB-rbcL LSC 792 0.0064 0.94 67.8 yes View details
rpl16-rps3 LSC 152 0.0314 1.00 66.7 yes View details
psaI-ycf4 LSC 403 0.0111 0.99 65.4 yes View details
rrn5-trnR-ACG SSC 287 0.0150 0.97 65.4 yes View details
petA-psbJ LSC 778 0.0065 1.00 65.2 yes View details
ycf3-trnS-GGA LSC 915 0.0066 1.00 64.9 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 85 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 505–526 1.000 83.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 519–540 1.000 82.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 518–539 1.000 82.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 520–541 1.000 82.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 506–527 1.000 82.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 946–974 1.000 80.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 945–973 1.000 80.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTCCTTGAAAAAGGCGCTCA 955–983 1.000 80.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC TTCCTTGAAAAAGGCGCTCA 932–960 1.000 78.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGCAGAGGTTTTTAAGGCA 893–921 1.000 78.2
atpI-atpH_p1 atpI-atpH CCCGTCATGTTCCTTGGATT ATAACGGAAGCGGCAGAAAT 1288–1307 1.000 83.4
atpI-atpH_p2 atpI-atpH CCCGTCATGTTCCTTGGATT TACCTTGACCAACTCCAGGT 1344–1363 1.000 82.6
atpI-atpH_p3 atpI-atpH CCCGTCATGTTCCTTGGATT AGCCAATCCAGCAGCAATAA 1304–1323 1.000 82.5
atpI-atpH_p4 atpI-atpH CCCGTCATGTTCCTTGGATT AATAACGGAAGCGGCAGAAA 1289–1308 1.000 82.2
atpI-atpH_p5 atpI-atpH CCCGTCATGTTCCTTGGATT GCAGTACCTTGACCAACTCC 1348–1367 1.000 82.0
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA CAACCACTCAGCCATCTCTC 805–1051 1.000 73.4
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA CAACCACTCAGCCATCTCTC 806–1052 1.000 73.4
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA ATGCTACGCTTTCAACCACT 817–1063 1.000 72.1
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA ATGCTACGCTTTCAACCACT 818–1064 1.000 72.1
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA GGATTCGAACCCTCGGTAAG 860–1106 1.000 71.7
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TCCTTTGCTACTCGGAGCTA AGAAGGTCTACGGTTCGAGT 1275–1359 1.000 83.8
ndhC-trnV-UAC_p2 ndhC-trnV-UAC ACTCGGAGCTAAAAATCCCG AGAAGGTCTACGGTTCGAGT 1266–1350 1.000 82.4
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TTCTCCGGTCCTTTGCTACT AGAAGGTCTACGGTTCGAGT 1283–1367 1.000 82.0
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TTTCTCCGGTCCTTTGCTAC AGAAGGTCTACGGTTCGAGT 1284–1368 1.000 81.1
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TCCTTTGCTACTCGGAGCTA GAAGGTCTACGGTTCGAGTC 1274–1358 1.000 81.0
atpB-rbcL_p1 atpB-rbcL CTGGCGGAAAAGCTACATCT CACCAGCTTTGAATCCAACAC 500–953 1.000 78.5
atpB-rbcL_p2 atpB-rbcL CTGGCGGAAAAGCTACATCT ACCAGCTTTGAATCCAACACT 501–952 1.000 78.2
atpB-rbcL_p3 atpB-rbcL GGCAACCCCAGAACTAGAAG CACCAGCTTTGAATCCAACAC 427–880 1.000 78.0
atpB-rbcL_p4 atpB-rbcL GATACGCCCCAGGTTCTTTT CACCAGCTTTGAATCCAACAC 457–910 1.000 77.8
atpB-rbcL_p5 atpB-rbcL GGCAACCCCAGAACTAGAAG ACCAGCTTTGAATCCAACACT 428–879 1.000 77.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (16)

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

Species Accession Length (bp) Link
Mikania additicia MT793849.1 151983 View on NCBI ↗
Mikania brevifaucia MT793850.1 152161 View on NCBI ↗
Mikania burchellii MT793851.1 151829 View on NCBI ↗
Mikania cordata NC_053251.1 151984 View on NCBI ↗
Mikania fasciculata MT793852.1 152070 View on NCBI ↗
Mikania glomerata MT793836.1 151773 View on NCBI ↗
Mikania haenkeana MT793837.1 151865 View on NCBI ↗
Mikania lehmannii MT793838.1 152062 View on NCBI ↗
Mikania micrantha NC_031833.1 152092 View on NCBI ↗
Mikania neurocaula MT793839.1 152045 View on NCBI ↗
Mikania oblongifolia MT793840.1 151845 View on NCBI ↗
Mikania obtusata MT793841.1 152106 View on NCBI ↗
Mikania purpurascens MT793853.1 152037 View on NCBI ↗
Mikania smaragdina MT793854.1 152020 View on NCBI ↗
Mikania sylvatica MT793855.1 152099 View on NCBI ↗
Mikania triangularis MT793845.1 151956 View on NCBI ↗