Markers + reference

Meconopsis

15 species · Papaveraceae · Ranunculales

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Species 15
Genome length 153–154 kb
Candidate markers 273
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 589 0.0426 0.99 82.0 yes View details
rps16-trnQ-UUG LSC 907 0.0417 1.00 85.7 yes View details
trnT-UGU-trnL-UAA LSC 622 0.0442 0.96 87.5 yes View details
accD-psaI LSC 467 0.0439 1.00 80.0 yes View details
ycf1 IRb 1095 0.0206 0.97 66.0 no View details
ndhF SSC 2220 0.0213 1.00 62.7 yes View details
ndhF-rpl32 SSC 963 0.0567 0.98 85.2 yes View details
rpl32-trnL-UAG SSC 613 0.0444 0.96 80.9 yes View details
rps15-ycf1 SSC 397 0.0448 0.97 79.7 yes View details
ycf1 SSC 5361 0.0293 1.00 66.8 yes View details
psaC-ndhE SSC 262 0.0528 1.00 83.6 yes View details
trnF-GAA-ndhJ LSC 749 0.0345 0.98 83.4 yes View details
petA-psbJ LSC 1073 0.0375 1.00 83.2 yes View details
ccsA-ndhD SSC 250 0.0689 0.99 82.9 yes View details
trnH-GUG-psbA LSC 239 0.0697 1.00 81.8 yes View details
psbM-trnD-GUC LSC 1128 0.0301 1.00 81.1 yes View details
rpoB-trnC-GCA LSC 961 0.0315 1.00 81.0 yes View details
ndhC-trnV-UAC LSC 1449 0.0330 1.00 80.4 yes View details
trnL-UAA-trnF-GAA LSC 360 0.0380 0.99 80.1 yes View details
atpH-atpI LSC 945 0.0246 1.00 79.6 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 TTCCCTCTAGACCTAGCTGC 305–386 0.933 87.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 319–400 0.933 87.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 318–399 0.933 87.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 320–401 0.933 87.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC TTCCCTCTAGACCTAGCTGC 310–391 0.933 83.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG CAAAAGGTATGTTGCTGCCG 1371–1526 0.933 89.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CAAAAGGTATGTTGCTGCCG 1370–1525 0.933 89.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 CTCGACCCATCCGTGAATTT CAAAAGGTATGTTGCTGCCG 1498–1653 0.933 89.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCGACCCATCCGTGAATTTC CAAAAGGTATGTTGCTGCCG 1497–1652 0.800 83.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGACCCATCCGTGAATTTCT CAAAAGGTATGTTGCTGCCG 1496–1651 0.800 83.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 980–1205 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 991–1216 1.000 89.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 984–1209 1.000 89.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 995–1220 1.000 88.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ACTCGGAGGTTCGAATCCTT 985–1210 1.000 87.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1002–1032 1.000 87.6
atpH-atpI_p2 atpH-atpI CGCAATACCTTCTACGGCTT CGAATCCATGGAGGGTCATC 1090–1120 1.000 87.3
atpH-atpI_p3 atpH-atpI CAGTACCTTGACCAACTCCG CGAATCCATGGAGGGTCATC 1061–1091 1.000 87.2
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 1003–1033 1.000 86.5
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC CGAATCCATGGAGGGTCATC 1062–1092 1.000 86.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATGAACCTGCAAAACCCCT AAAAGGATTTGCAGTCCCCC 1020–1143 1.000 88.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ACCTGCAAAACCCCTCAAAT AAAAGGATTTGCAGTCCCCC 1015–1138 1.000 88.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AACCTGCAAAACCCCTCAAA AAAAGGATTTGCAGTCCCCC 1016–1139 1.000 88.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CAATGAACCTGCAAAACCCC AAAAGGATTTGCAGTCCCCC 1021–1144 1.000 87.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCTGATCAATGAACCTGCA AAAAGGATTTGCAGTCCCCC 1094 0.067 38.8
psbM-trnD-GUC_p1 psbM-trnD-GUC ATGAACAGCGCAGTAGCAAT TTCAATTGGTCAGAGCACCG 914–1247 1.000 86.1
psbM-trnD-GUC_p2 psbM-trnD-GUC TGAACAGCGCAGTAGCAATA TTCAATTGGTCAGAGCACCG 913–1246 1.000 85.2
psbM-trnD-GUC_p3 psbM-trnD-GUC AATGAACAGCGCAGTAGCAA TTCAATTGGTCAGAGCACCG 915–1248 1.000 84.4
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGCGCAGTAGC TTCAATTGGTCAGAGCACCG 917–1250 1.000 83.1
psbM-trnD-GUC_p5 psbM-trnD-GUC ACTAGAATGAACAGCGCAGT TTCAATTGGTCAGAGCACCG 920–1253 1.000 82.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Meconopsis bella NC_080898.1 153073 View on NCBI ↗
Meconopsis betonicifolia PP542026.1 152973 View on NCBI ↗
Meconopsis biluoensis OR774891.1 154276 View on NCBI ↗
Meconopsis georgei OR774904.1 153654 View on NCBI ↗
Meconopsis henrici NC_050877.1 153788 View on NCBI ↗
Meconopsis horridula NC_056967.1 153761 View on NCBI ↗
Meconopsis integrifolia NC_061607.1 152939 View on NCBI ↗
Meconopsis paniculata NC_085733.1 152887 View on NCBI ↗
Meconopsis pinnatifolia NC_085732.1 153557 View on NCBI ↗
Meconopsis pseudohorridula NC_061608.1 154190 View on NCBI ↗
Meconopsis punicea NC_050878.1 153281 View on NCBI ↗
Meconopsis racemosa NC_039625.1 153763 View on NCBI ↗
Meconopsis racemosa var. racemosa NC_061609.1 153973 View on NCBI ↗
Meconopsis simplicifolia NC_070211.1 152772 View on NCBI ↗
Meconopsis torquata NC_086706.1 153290 View on NCBI ↗