Markers + reference

Papaver

15 species · Papaveraceae · Ranunculales

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Species 15
Genome length 153–154 kb
Candidate markers 257
Primer pairs 100

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 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1081 0.0366 1.00 78.1 yes View details
trnT-GGU-psbD LSC 1300 0.0346 1.00 70.3 yes View details
ndhC-trnM-CAU LSC 2228 0.0269 1.00 67.8 yes View details
accD-psaI LSC 478 0.0475 1.00 74.9 yes View details
petA-psbJ LSC 1053 0.0432 1.00 74.4 yes View details
trnN-GUU-ndhF IRb 1852 0.0203 1.00 60.1 yes View details
ndhF-rpl32 SSC 1042 0.0429 1.00 75.1 yes View details
rpl32-trnL-UAG SSC 582 0.0568 1.00 77.2 yes View details
rps15-ycf1 SSC 397 0.0503 1.00 71.8 yes View details
ycf1 SSC 5352 0.0306 1.00 66.7 yes View details
trnE-UUC-trnT-GGU LSC 451 0.0453 1.00 74.4 yes View details
trnD-GUC-trnY-GUA LSC 369 0.0313 1.00 70.2 yes View details
trnF-GAA-ndhJ LSC 750 0.0322 1.00 69.5 yes View details
psbI-trnS-GCU LSC 151 0.0512 1.00 68.8 yes View details
rpoB-trnC-GCA LSC 995 0.0305 1.00 68.2 yes View details
psbE-petL LSC 1245 0.0273 1.00 67.5 yes View details
trnH-GUG-psbA LSC 243 0.0503 1.00 67.2 yes View details
psbM-trnD-GUC LSC 1036 0.0312 1.00 66.6 yes View details
ccsA-ndhD SSC 242 0.0430 1.00 66.6 yes View details
psaJ-rpl33 LSC 390 0.0322 0.99 65.9 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 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 TCACAATCCACTGCCTTCAC TTCCCTCTAGACCTAGCTGC 323–328 0.667 69.1
trnH-GUG-psbA_p2 trnH-GUG-psbA TCACAATCCACTGCCTTCAC GTTGACAGTCAAGGTCGTGT 419–424 0.667 68.3
trnH-GUG-psbA_p3 trnH-GUG-psbA TCACAATCCACTGCCTTCAC TTGTAGCCGCTCATGGTTAC 595–600 0.667 67.8
trnH-GUG-psbA_p4 trnH-GUG-psbA TCACAATCCACTGCCTTCAC ATATTCCGCTCCTGTTGCAG 900–905 0.667 67.0
trnH-GUG-psbA_p5 trnH-GUG-psbA TCACAATCCACTGCCTTCAC CCCAATTGGTCAAGGAAGCT 855–860 0.667 66.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1175–1207 1.000 90.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1154–1186 1.000 89.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1165–1197 1.000 89.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACCGATCATGTCCTT CTCGGAGGTTCGAATCCTTC 1179–1211 1.000 88.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1158–1190 1.000 88.8
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA TTCGAATCCCTCTCTTTCCG 191–217 1.000 77.1
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA GGGTTCGAATCCCTCTCTTT 194–220 1.000 76.1
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA GGGTTCGAATCCCTCTCTTTC 194–220 1.000 76.1
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA GGTTCGAATCCCTCTCTTTCC 193–219 1.000 76.1
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCTGGACGTGAGGAA TTCGAATCCCTCTCTTTCCG 190–216 1.000 73.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CTCTGCTTCTTGCTTTTGCC 1659–1662 0.667 66.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCGGGGCTTTGCAATATTTG CTCTGCTTCTTGCTTTTGCC 1539–1542 0.667 66.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TTCTCTCTTGGGTCCTAGGC 1749–1752 0.667 66.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AATCTTCCTCCCCAATCGGA CTCTGCTTCTTGCTTTTGCC 1620–1623 0.667 66.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATCTTCCTCCCCAATCGGAT CTCTGCTTCTTGCTTTTGCC 1619–1622 0.667 65.9
psbM-trnD-GUC_p1 psbM-trnD-GUC TGCGAGAATATTTACTTCCA TTCAATTGGTCAGAGCACCG 1121–1213 1.000 48.8
psbM-trnD-GUC_p2 psbM-trnD-GUC ATGCGAGAATATTTACTTCCA TTCAATTGGTCAGAGCACCG 1122–1214 1.000 48.8
psbM-trnD-GUC_p3 psbM-trnD-GUC TGCGAGAATATTTACTTCCAT TTCAATTGGTCAGAGCACCG 1121–1213 1.000 48.8
psbM-trnD-GUC_p4 psbM-trnD-GUC TGCGAGAATATTTACTTCCA GTTCAATTGGTCAGAGCACC 1122–1214 1.000 48.8
psbM-trnD-GUC_p5 psbM-trnD-GUC AATGCGAGAATATTTACTTCCA TTCAATTGGTCAGAGCACCG 1123–1215 1.000 48.7
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA TGACGGATTCATCGGATCCT TGGATTCTTCCTGGGTCGAT 546–563 1.000 85.7
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA TGAGTTGACGGATTCATCGG ATGGATTCTTCCTGGGTCGA 552–569 1.000 85.6
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA TGAGTTGACGGATTCATCGG TGGATTCTTCCTGGGTCGAT 551–568 1.000 85.6
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA TGACGGATTCATCGGATCCT ATGGATTCTTCCTGGGTCGA 547–564 1.000 85.6
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA TTCATCGGATCCTAGGTCGG TGGATTCTTCCTGGGTCGAT 539–556 1.000 85.1

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
Papaver alboroseum NC_065204.1 153703 View on NCBI ↗
Papaver dubium NC_065205.1 152909 View on NCBI ↗
Papaver hultenii NC_065206.1 153812 View on NCBI ↗
Papaver hultenii var. salmonicolor OM174283.1 153668 View on NCBI ↗
Papaver keelei NC_065207.1 153848 View on NCBI ↗
Papaver lapponicum NC_065208.1 153817 View on NCBI ↗
Papaver mcconnellii NC_065209.1 153687 View on NCBI ↗
Papaver nudicaule NC_063713.1 153903 View on NCBI ↗
Papaver orientale NC_037832.1 152799 View on NCBI ↗
Papaver pseudo-orientale NC_065210.1 152954 View on NCBI ↗
Papaver radicatum subsp. dahlianum OM174290.1 153747 View on NCBI ↗
Papaver radicatum subsp. laestadianum OM174291.1 153767 View on NCBI ↗
Papaver radicatum subsp. macrostigmum OM174292.1 153767 View on NCBI ↗
Papaver rhoeas NC_037831.1 152905 View on NCBI ↗
Papaver somniferum subsp. setigerum OM174294.1 152862 View on NCBI ↗