Markers + reference

Corydalis

49 species · Papaveraceae · Ranunculales

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Species 49
Genome length 159–213 kb
Candidate markers 291
Primer pairs 85

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 291 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnV-UAC-rps16 LSC 1122 0.4428 0.88 72.3 yes View details
pafI-trnS-GGA LSC 1386 0.2599 0.98 76.8 yes View details
ndhC-psaI LSC 2266 0.3258 0.79 73.5 yes View details
clpP1 LSC 2235 0.1575 0.97 80.5 yes View details
ndhF-rpl32 IRb 2539 0.2006 0.83 73.1 yes View details
ycf1-rps15 IRa 2402 0.3108 0.29 63.9 yes View details
rpl32-ndhF IRa 2539 0.1938 0.84 73.0 yes View details
trnC-GCA-petN LSC 871 0.0671 0.98 82.7 yes View details
trnT-UGU-trnL-UAA LSC 667 0.0730 0.97 81.2 yes View details
trnE-UUC-trnT-GGU LSC 565 0.0680 0.98 80.7 yes View details
ndhD IRb 1509 0.0517 1.00 80.7 yes View details
trnT-GGU-psbD LSC 901 0.0579 0.99 80.4 yes View details
psaA-pafI LSC 629 0.0513 0.98 80.2 yes View details
ndhD IRa 1509 0.0522 1.00 80.0 yes View details
trnS-GCU-trnG-UCC LSC 1009 0.0779 0.94 79.7 yes View details
psbE-petL LSC 1230 0.0573 0.99 79.6 yes View details
rpoB-trnC-GCA LSC 1241 0.0729 0.97 79.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnV-UAC-rps16_p1 trnV-UAC-rps16 TAGGCTACAAATGGACCCCA CCACCGAGATTGTTCACGAT 640–1683 0.306 64.0
trnV-UAC-rps16_p2 trnV-UAC-rps16 AGCTTGACTTTTGGTTCGGT CCACCGAGATTGTTCACGAT 678–1722 0.306 63.7
trnV-UAC-rps16_p3 trnV-UAC-rps16 GGTTCGAATCCGTATAGCCC CCACCGAGATTGTTCACGAT 188–1231 0.306 63.6
trnV-UAC-rps16_p4 trnV-UAC-rps16 TAGGCTACAAATGGACCCCA GGGCTGTGTGAGAAACTTCA 1506–1651 0.265 55.8
trnV-UAC-rps16_p5 trnV-UAC-rps16 AGCTTGACTTTTGGTTCGGT GGGCTGTGTGAGAAACTTCA 1545–1690 0.265 55.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 550–1151 1.000 62.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AGAACGAATCACACTTTTACCAC 553–1154 1.000 61.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GAACGAATCACACTTTTACCACT 552–1153 1.000 61.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACGAATCACACTTTTACCACT 551–1152 1.000 60.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 536–1137 1.000 58.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TTGTTGTTGATCAGGCGACA 1797–1878 0.878 86.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCCTTAGGGTCCAACTCTGA AGAATCCTTCCTTGGAGCCT 1915–1976 0.449 69.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTTAGGGTCCAACTCTG AGAATCCTTCCTTGGAGCCT 1916–1977 0.449 69.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCGGGGCTTTGCAATATTTG AGAATCCTTCCTTGGAGCCT 1882–1943 0.449 69.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT AGAATCCTTCCTTGGAGCCT 2002–2063 0.429 68.8
trnC-GCA-petN_p1 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 792–975 1.000 89.1
trnC-GCA-petN_p2 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC TTAAAGCAGCCCAAGCAAGA 767–950 1.000 88.1
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCAAGACTTACT 786–969 0.980 86.8
trnC-GCA-petN_p4 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC CAGCCCAAGCAAGACTTACT 761–944 0.980 85.8
trnC-GCA-petN_p5 trnC-GCA-petN TTCAAATCTGGGTGTCGCC TTAAAGCAGCCCAAGCAAGA 765–948 1.000 83.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TACCGCTGAGTTAAAAGGGC 382–641 1.000 89.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA TACCGCTGAGTTAAAAGGGC 361–620 1.000 88.9
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CCTGAACCACTAGACGATGG TACCGCTGAGTTAAAAGGGC 358–617 1.000 86.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CTGAACCACTAGACGATGGG TACCGCTGAGTTAAAAGGGC 357–616 1.000 86.5
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGAACCACTAGACGATGGGG TACCGCTGAGTTAAAAGGGC 356–615 1.000 84.7
trnT-GGU-psbD_p1 trnT-GGU-psbD GTTCAAATCCGATAAGGGGCT TCTACCAAGGGCTATTGTCA 927–964 0.980 62.9
trnT-GGU-psbD_p2 trnT-GGU-psbD TTCAAATCCGATAAGGGGCT TCTACCAAGGGCTATTGTCA 926–963 0.980 60.1
trnT-GGU-psbD_p3 trnT-GGU-psbD GTTCAAATCCGATAAGGGGC TCTACCAAGGGCTATTGTCA 927–964 0.980 59.9
trnT-GGU-psbD_p4 trnT-GGU-psbD GTTCAAATCCGATAAGGGGCT ATCTACCAAGGGCTATTGTCA 928–965 0.980 59.6
trnT-GGU-psbD_p5 trnT-GGU-psbD GTTCAAATCCGATAAGGGGCT TCTACCAAGGGCTATTGTCAT 927–964 0.980 59.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (49)

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

Species Accession Length (bp) Link
Corydalis alata NC_072196.1 190434 View on NCBI ↗
Corydalis balansae NC_066120.1 186692 View on NCBI ↗
Corydalis bonghwaensis NC_072203.1 188863 View on NCBI ↗
Corydalis borii NC_066107.1 175200 View on NCBI ↗
Corydalis capnoides BK063227.1 199294 View on NCBI ↗
Corydalis casimiriana subsp. brachycarpa ON152777.1 170647 View on NCBI ↗
Corydalis chrysosphaera MZ983401.1 200923 View on NCBI ↗
Corydalis conspersa NC_047208.1 187810 View on NCBI ↗
Corydalis cornupetala NC_072189.1 184406 View on NCBI ↗
Corydalis cornuta NC_066108.1 182423 View on NCBI ↗
Corydalis crispa NC_066105.1 176726 View on NCBI ↗
Corydalis curviflora NC_066103.1 182286 View on NCBI ↗
Corydalis dasyptera OR134581.1 187898 View on NCBI ↗
Corydalis davidii NC_057184.1 165416 View on NCBI ↗
Corydalis elata NC_066119.1 184576 View on NCBI ↗
Corydalis fargesii NC_066114.1 173795 View on NCBI ↗
Corydalis filistipes NC_072190.1 189459 View on NCBI ↗
Corydalis grandicalyx NC_072198.1 189792 View on NCBI ↗
Corydalis hallaisanensis NC_072184.1 186162 View on NCBI ↗
Corydalis hamata NC_066128.1 188443 View on NCBI ↗
Corydalis hendersonii NC_066106.1 168116 View on NCBI ↗
Corydalis hendersonii var. altocristata OR134585.1 194676 View on NCBI ↗
Corydalis humilis NC_072197.1 186583 View on NCBI ↗
Corydalis impatiens NC_060862.1 197317 View on NCBI ↗
Corydalis incisa NC_066121.1 213295 View on NCBI ↗
Corydalis intermedia BK063235.1 184999 View on NCBI ↗
Corydalis jingyuanensis NC_066118.1 181730 View on NCBI ↗
Corydalis livida NC_066123.1 189569 View on NCBI ↗
Corydalis maculata NC_072186.1 185060 View on NCBI ↗
Corydalis melanochlora NC_066112.1 187673 View on NCBI ↗
Corydalis minutiflora NC_066110.1 182537 View on NCBI ↗
Corydalis misandra NC_072199.1 186851 View on NCBI ↗
Corydalis mucronata NC_066122.1 191405 View on NCBI ↗
Corydalis namdoensis NC_072195.1 184889 View on NCBI ↗
Corydalis ohii NC_072191.1 186724 View on NCBI ↗
Corydalis ophiocarpa OR164892.1 186770 View on NCBI ↗
Corydalis pauciovulata NC_072192.1 159167 View on NCBI ↗
Corydalis petrophila NC_066113.1 183272 View on NCBI ↗
Corydalis racemosa NC_066116.1 190073 View on NCBI ↗
Corydalis raddeana NC_072200.1 182287 View on NCBI ↗
Corydalis remota NC_072183.1 186899 View on NCBI ↗
Corydalis repens PV658157.1 188101 View on NCBI ↗
Corydalis retingensis NC_066125.1 205542 View on NCBI ↗
Corydalis saxicola NC_057186.1 188060 View on NCBI ↗
Corydalis solida BK063234.1 185904 View on NCBI ↗
Corydalis temulifolia NC_050996.1 194096 View on NCBI ↗
Corydalis turtschaninovii NC_072185.1 195713 View on NCBI ↗
Corydalis wandoensis NC_072187.1 188610 View on NCBI ↗
Corydalis yanhusuo NC_065384.1 213124 View on NCBI ↗