Markers + reference

Hylomecon

2 species · Papaveraceae · Ranunculales

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Species 2
Genome length 160–160 kb
Candidate markers 270
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 387 0.0413 1.00 70.6 yes View details
rps16-trnQ-UUG LSC 1877 0.0091 1.00 58.1 yes View details
petN-psbM LSC 1193 0.0101 0.99 62.3 yes View details
trnT-UGU-trnL-UAA LSC 695 0.0159 0.99 68.6 yes View details
ndhK LSC 747 0.0040 1.00 49.5 yes View details
petA-psbJ LSC 1161 0.0121 0.99 52.1 yes View details
petB LSC 1452 0.0131 1.00 55.2 yes View details
ndhF-rpl32 SSC 983 0.0112 0.99 53.8 yes View details
rpl32-trnL-UAG SSC 897 0.0104 0.96 57.2 yes View details
ndhD SSC 1503 0.0060 1.00 55.6 yes View details
ycf1 SSC 5529 0.0040 1.00 42.5 yes View details
psbT-psbN LSC 64 0.0312 1.00 70.5 yes View details
ndhJ-ndhK LSC 114 0.0439 1.00 68.1 yes View details
ccsA-ndhD SSC 214 0.0280 1.00 65.2 yes View details
psaI-ycf4 LSC 442 0.0047 0.96 61.6 yes View details
ndhG-ndhI SSC 393 0.0103 0.99 61.6 yes View details
ycf3-trnS-GGA LSC 738 0.0041 1.00 61.5 yes View details
psbM-trnD-GUC LSC 1124 0.0044 1.00 61.3 yes View details
rps2-rpoC2 LSC 212 0.0142 1.00 61.1 yes View details
atpB-rbcL LSC 731 0.0041 1.00 61.1 yes View details
atpF LSC 1282 0.0031 1.00 60.5 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 105 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 CCTCTAGACCTAGCTGCTGT 454 1.000 81.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 457 1.000 81.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 468 1.000 81.1
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 467 1.000 81.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 469 1.000 81.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1968–1983 1.000 79.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1966–1981 1.000 79.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1974–1989 1.000 79.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1975–1990 1.000 79.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCGAGCTAAGAGCACCTTC GAGGTTCGAATCCTTCCGTC 2021–2036 1.000 79.4
atpF_p1 atpF TTCGTCGGCTCTAATGGTTG ACGAAGTGATACAAAACGAACTC 1429–1440 1.000 51.6
atpF_p2 atpF GGCTCTAATGGTTGCCATGA ACGAAGTGATACAAAACGAACTC 1423–1434 1.000 51.2
atpF_p3 atpF TTCGTCGGCTCTAATGGTTG ACGAAGTGATACAAAACGAACT 1429–1440 1.000 50.9
atpF_p4 atpF GGCTCTAATGGTTGCCATGA ACGAAGTGATACAAAACGAACT 1423–1434 1.000 50.5
atpF_p5 atpF TTCGTCGGCTCTAATGGTTG CGAAGTGATACAAAACGAACTCT 1428–1439 1.000 49.6
rps2-rpoC2_p1 rps2-rpoC2 TTGCAGAGATGTAAGGTGCC CCATCAGAACAATCATTTCCAGG 362–363 1.000 53.9
rps2-rpoC2_p2 rps2-rpoC2 TTGCAGAGATGTAAGGTGCC TCCATGATCCATCAGAACAATCA 370–371 1.000 52.9
rps2-rpoC2_p3 rps2-rpoC2 GCAGAGATGTAAGGTGCCAT CCATCAGAACAATCATTTCCAGG 360–361 1.000 52.1
rps2-rpoC2_p4 rps2-rpoC2 GCAGAGATGTAAGGTGCCAT TCCATGATCCATCAGAACAATCA 368–369 1.000 51.1
rps2-rpoC2_p5 rps2-rpoC2 TTGCAGAGATGTAAGGTGCC TGCATCCAAAAGAATTTCCATGA 386–387 1.000 50.0
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA GCCACTGCACTGTTCATTCT 1341–1347 1.000 75.1
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG GCCACTGCACTGTTCATTCT 1347–1353 1.000 73.7
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCCACTGCACTGTTCATTC 1342–1348 1.000 72.8
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT GCCACTGCACTGTTCATTCT 1287–1293 1.000 72.4
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCCACTGCACTGTTCATT 1342–1348 1.000 72.3
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTGGC TTCAATTGGTCAGAGCACCG 1235–1279 1.000 70.4
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTGGC GTTCAATTGGTCAGAGCACC 1236–1280 1.000 66.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTGGC TCAATTGGTCAGAGCACCG 1234–1278 1.000 64.4
psbM-trnD-GUC_p4 psbM-trnD-GUC TAGAATGAACAGTGCAGTGGC TTCAATTGGTCAGAGCACCG 1236–1280 1.000 63.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTGGC AGTTCAATTGGTCAGAGCACC 1237–1281 1.000 62.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Hylomecon japonica NC_045388.1 160011 View on NCBI ↗
Hylomecon japonica var. dissecta MN756858.1 159942 View on NCBI ↗