Markers + reference

Hieracium

10 species · Asteraceae · Asterales

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Species 10
Genome length 153–153 kb
Candidate markers 271
Primer pairs 85

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 9 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 418 0.0105 0.97 49.4 yes View details
rps16-trnQ-UUG LSC 971 0.0074 0.98 62.8 yes View details
trnC-GCA-petN LSC 850 0.0072 0.99 47.7 yes View details
ndhC-trnV-UAC LSC 1216 0.0050 0.97 56.6 yes View details
ycf1 IRb 495 0.0013 1.00 33.5 no View details
ndhF-rpl32 SSC 1096 0.0057 0.99 61.3 yes View details
rpl32-trnL SSC 816 0.0086 1.00 66.9 yes View details
ccsA SSC 969 0.0024 1.00 37.3 yes View details
rps15-ycf1 SSC 412 0.0081 1.00 45.6 yes View details
ycf1 SSC 5028 0.0047 1.00 42.3 yes View details
rps19-trnH-GUG LSC 39 0.2131 0.59 61.2 no View details
trnK-UUU-rps16 LSC 816 0.0052 1.00 58.6 yes View details
psaA-ycf3 LSC 753 0.0044 0.98 57.7 yes View details
petA-psbJ LSC 816 0.0036 1.00 55.3 yes View details
rpl20-rps12 LSC 747 0.0041 1.00 54.8 yes View details
rpl16 LSC 1439 0.0027 1.00 54.7 yes View details
rps16 LSC 1119 0.0037 1.00 53.7 yes View details
trnF-ndhJ LSC 574 0.0069 1.00 53.7 yes View details
psbE-petL LSC 1277 0.0033 1.00 53.4 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 512–547 1.000 82.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 526–561 1.000 82.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 525–560 1.000 82.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 527–562 1.000 82.6
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 513–548 1.000 82.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TTCCTTGAAAAAGGCGCTCA 1012–1045 1.000 79.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TTCCTTGAAAAAGGCGCTCA 1011–1044 1.000 79.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGCGCTCA 952–985 1.000 78.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGCGCTCA 951–984 1.000 78.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTCCTTGAAAAAGGCGCTCA 1036–1069 1.000 78.2
rps16_p1 rps16 AGAAATCACTATCCTACCCTTAGTT TCTCTGTACCGACTGAACCA 1237–1244 1.000 41.2
rps16_p2 rps16 AGAAATCACTATCCTACCCTTAGT TCTCTGTACCGACTGAACCA 1237–1244 0.900 37.1
rps16_p3 rps16 AGAAATCACTATCCTACCCT TCTCTGTACCGACTGAACCA 1237–1244 0.900 37.1
rps16_p4 rps16 AGAAATCACTATCCTACCCTT TCTCTGTACCGACTGAACCA 1237–1244 0.900 37.1
rps16_p5 rps16 AGAAATCACTATCCTACCCTTAGT GTCTCTGTACCGACTGAACC 1238–1245 0.900 37.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1039–1062 1.000 81.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1054–1077 1.000 79.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1053–1076 1.000 79.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1043–1066 1.000 76.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1069–1092 1.000 76.7
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 891–906 1.000 81.2
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 909–924 1.000 78.9
trnC-GCA-petN_p3 trnC-GCA-petN TAGTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 947–962 1.000 76.5
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 890–905 1.000 75.2
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 899–914 1.000 75.1
psaA-ycf3_p1 psaA-ycf3 GAGAAATGACCCGGTCTAGC AGCCGCTGAGTATTGGAAAC 924–945 1.000 78.8
psaA-ycf3_p2 psaA-ycf3 GAGAAATGACCCGGTCTAGC CAAGCCGCTGAGTATTGGAA 926–947 1.000 78.8
psaA-ycf3_p3 psaA-ycf3 GAGAAATGACCCGGTCTAGC AAGCCGCTGAGTATTGGAAA 925–946 1.000 77.0
psaA-ycf3_p4 psaA-ycf3 TTTTACTTCTGGTTCCGGCG AGCCGCTGAGTATTGGAAAC 859–880 1.000 77.0
psaA-ycf3_p5 psaA-ycf3 TTTTACTTCTGGTTCCGGCG CAAGCCGCTGAGTATTGGAA 861–882 1.000 77.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Hieracium alpinum OR909634.1 152987 View on NCBI ↗
Hieracium amplexicaule OR909635.1 153038 View on NCBI ↗
Hieracium atratum OR909636.1 152644 View on NCBI ↗
Hieracium bifidum OR909637.1 152648 View on NCBI ↗
Hieracium bupleuroides OR909638.1 153177 View on NCBI ↗
Hieracium glanduliferum OR909639.1 152894 View on NCBI ↗
Hieracium lachenalii OR909640.1 153203 View on NCBI ↗
Hieracium murorum OR909641.1 152645 View on NCBI ↗
Hieracium umbrosum OR909642.1 152656 View on NCBI ↗
Hieracium villosum OR909643.1 153195 View on NCBI ↗