Markers + reference

Aquilegia

70 species · Ranunculaceae · Ranunculales

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Species 70
Genome length 160–162 kb
Candidate markers 287
Primer pairs 85

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 7 remaining regions by MarkerSeek score (out of 287 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-rpl16 LSC 220 0.0130 1.00 50.8 yes View details
trnK-UUU-rps16 LSC 642 0.0074 1.00 64.6 yes View details
rps16-trnQ-UUG LSC 1128 0.0037 1.00 57.2 yes View details
trnT-GGU-psbD LSC 1338 0.0036 1.00 53.6 yes View details
clpP-rps12 LSC 1219 0.0063 1.00 60.2 yes View details
rpl36-trnN-GUU LSC 655 0.0043 0.99 51.7 yes View details
trnN-GUU-infA LSC 519 0.0112 0.99 63.1 yes View details
ycf1-ndhF SSC 779 0.0135 0.98 64.0 yes View details
ndhF-rpl32 SSC 851 0.0090 0.99 60.0 yes View details
rpl32-trnL-UAG SSC 427 0.0094 1.00 58.9 yes View details
rpl23-trnH-GUG LSC 297 0.0193 0.95 62.3 no View details
rpl2-rpl23 IRb 47 0.0145 1.00 60.9 yes View details
accD-trnG-GCC LSC 1341 0.0021 1.00 58.4 yes View details
psbM-trnD-GUC LSC 1098 0.0039 1.00 54.8 yes View details
trnF-GAA-ndhJ LSC 580 0.0038 0.99 53.7 yes View details
psbT-psbN LSC 95 0.0091 1.00 53.2 yes View details
rpl16-rps3 LSC 159 0.0116 1.00 52.1 yes View details
petN-psbM LSC 1144 0.0022 1.00 52.0 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-rpl16_p1 trnH-GUG-rpl16 TGAAATAGGATGGGCGAACG CGAAATCGGATGCTTTTGGG 320–352 0.986 86.7
trnH-GUG-rpl16_p2 trnH-GUG-rpl16 CAATCCACTGCCTTCATCCA CGAAATCGGATGCTTTTGGG 269–301 0.986 86.7
trnH-GUG-rpl16_p3 trnH-GUG-rpl16 AATCCACTGCCTTCATCCAC CGAAATCGGATGCTTTTGGG 268–300 0.986 86.7
trnH-GUG-rpl16_p4 trnH-GUG-rpl16 ACAATCCACTGCCTTCATCC CGAAATCGGATGCTTTTGGG 270–302 0.986 86.7
trnH-GUG-rpl16_p5 trnH-GUG-rpl16 AAATAGGATGGGCGAACGAC CGAAATCGGATGCTTTTGGG 318–350 0.986 86.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCCTTGAAAAAGGCGCG 671–791 1.000 87.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCCTTGAAAAAGGCGCG 670–790 1.000 87.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTACCAACGGTATGGACGA ATTTCCTTGAAAAAGGCGCG 736–856 1.000 87.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC ATTTCCTTGAAAAAGGCGCG 685–805 1.000 86.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA ATTTCCTTGAAAAAGGCGCG 680–800 1.000 86.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AGAACCCACAACCGATCATG GAGGTTCGAATCCTTCCGTC 1217–1239 1.000 83.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1212–1234 1.000 83.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGAGCACCTCAGAATTCC GAGGTTCGAATCCTTCCGTC 1260–1282 1.000 83.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1191–1213 1.000 83.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AACCCACAACCGATCATGTC GAGGTTCGAATCCTTCCGTC 1215–1237 1.000 83.3
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 1287–1315 1.000 71.7
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 1293–1321 1.000 70.2
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1233–1261 1.000 69.0
petN-psbM_p4 petN-psbM GGGGGCATAATTCACATGGA TGCTACTGCACTGTTCATTCT 1316–1344 1.000 68.7
petN-psbM_p5 petN-psbM AGGGGGCATAATTCACATGG TGCTACTGCACTGTTCATTCT 1317–1345 1.000 68.6
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1190–1219 1.000 63.1
psbM-trnD-GUC_p2 psbM-trnD-GUC TTGACTGACCGTTTTTACGT TTCAATTGGTCAGAGCACCG 1239–1268 1.000 61.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TTCAATTGGTCAGAGCACCG 1197–1226 1.000 59.9
psbM-trnD-GUC_p4 psbM-trnD-GUC TTTGACTGACCGTTTTTACGT TTCAATTGGTCAGAGCACCG 1240–1269 1.000 59.5
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 1191–1220 1.000 58.9
trnT-GGU-psbD_p1 trnT-GGU-psbD TGTCTTCACGTTGGCTCATT GGGAAAGAGCAATAGACCGG 1525–1584 1.000 81.9
trnT-GGU-psbD_p2 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGGAAAGAGCAATAGACCGG 1454–1513 1.000 81.9
trnT-GGU-psbD_p3 trnT-GGU-psbD CCCCTTTAACTCAGCGGTAG GGGAAAGAGCAATAGACCGG 1490–1549 1.000 81.5
trnT-GGU-psbD_p4 trnT-GGU-psbD TGTCTTCACGTTGGCTCATT ACAAAAACGAAACGGTCCCT 1497–1556 1.000 80.3
trnT-GGU-psbD_p5 trnT-GGU-psbD TGTCTTCACGTTGGCTCATT GACCGGACCAACCTACAAAA 1511–1570 1.000 80.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (70)

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

Species Accession Length (bp) Link
Aquilegia alpina PV564728.1 161345 View on NCBI ↗
Aquilegia amurensis PV564729.1 160406 View on NCBI ↗
Aquilegia apuana PV564730.1 161573 View on NCBI ↗
Aquilegia aradanica PV564731.1 160973 View on NCBI ↗
Aquilegia atrata PV564732.1 161344 View on NCBI ↗
Aquilegia atrovinosa PV564733.1 161860 View on NCBI ↗
Aquilegia barbaricina PV564735.1 161475 View on NCBI ↗
Aquilegia barnebyi NC_053820.1 161954 View on NCBI ↗
Aquilegia barykinae PV564737.1 159782 View on NCBI ↗
Aquilegia bertolonii PV564738.1 161366 View on NCBI ↗
Aquilegia borodinii PV564739.1 161270 View on NCBI ↗
Aquilegia brevistyla PV564740.1 162202 View on NCBI ↗
Aquilegia buergeriana PV564741.1 161451 View on NCBI ↗
Aquilegia canadensis PV564743.1 161929 View on NCBI ↗
Aquilegia champagnatii PV564745.1 161577 View on NCBI ↗
Aquilegia chrysantha PV564746.1 161900 View on NCBI ↗
Aquilegia colchica PV564749.1 161518 View on NCBI ↗
Aquilegia cossoniana PV564750.1 161327 View on NCBI ↗
Aquilegia daingolica PV564751.1 161275 View on NCBI ↗
Aquilegia dumeticola PV564752.1 161500 View on NCBI ↗
Aquilegia ecalcarata NC_041529.1 161795 View on NCBI ↗
Aquilegia einseleana PV564754.1 161549 View on NCBI ↗
Aquilegia elegantula PV564755.1 161854 View on NCBI ↗
Aquilegia eximia PV564756.1 161745 View on NCBI ↗
Aquilegia flabellata PV564757.1 160083 View on NCBI ↗
Aquilegia flavescens PV564758.1 162025 View on NCBI ↗
Aquilegia formosa PV564759.1 161842 View on NCBI ↗
Aquilegia fragrans PV564760.1 162014 View on NCBI ↗
Aquilegia gegica PV564761.1 161537 View on NCBI ↗
Aquilegia glandulosa PV564762.1 161021 View on NCBI ↗
Aquilegia grata PV564763.1 161578 View on NCBI ↗
Aquilegia hebeica PV564764.1 160521 View on NCBI ↗
Aquilegia incurvata PV564765.1 162480 View on NCBI ↗
Aquilegia iulia PV564766.1 161525 View on NCBI ↗
Aquilegia japonica PV564767.1 161474 View on NCBI ↗
Aquilegia jonesii PV564768.1 162276 View on NCBI ↗
Aquilegia jucunda PV564769.1 160997 View on NCBI ↗
Aquilegia kansuensis NC_058528.1 162090 View on NCBI ↗
Aquilegia karelinii PV564771.1 161765 View on NCBI ↗
Aquilegia kubanica PV564772.1 161104 View on NCBI ↗
Aquilegia lactiflora PV564747.1 161821 View on NCBI ↗
Aquilegia laramiensis PV564774.1 161985 View on NCBI ↗
Aquilegia longissima PV564775.1 162086 View on NCBI ↗
Aquilegia lucensis PV564776.1 161574 View on NCBI ↗
Aquilegia magellensis PV564777.1 161328 View on NCBI ↗
Aquilegia moorcroftiana PV564778.1 161995 View on NCBI ↗
Aquilegia nigricans PV564780.1 161361 View on NCBI ↗
Aquilegia nugorensis PV564781.1 161745 View on NCBI ↗
Aquilegia nuragica PV564782.1 161473 View on NCBI ↗
Aquilegia olympica PV564783.1 161499 View on NCBI ↗
Aquilegia oxysepala PV564784.1 161442 View on NCBI ↗
Aquilegia pubescens PV564785.1 162132 View on NCBI ↗
Aquilegia pubiflora PV564786.1 161941 View on NCBI ↗
Aquilegia reuteri PV564787.1 161353 View on NCBI ↗
Aquilegia saximontana PV564789.1 162074 View on NCBI ↗
Aquilegia shockleyi PV564790.1 161894 View on NCBI ↗
Aquilegia sibirica PV564791.1 161372 View on NCBI ↗
Aquilegia sicula PV564792.1 161378 View on NCBI ↗
Aquilegia skinneri PV564793.1 162188 View on NCBI ↗
Aquilegia synakensis PV564794.1 161422 View on NCBI ↗
Aquilegia thalictrifolia PV564795.1 161549 View on NCBI ↗
Aquilegia turczaninovii PV564796.1 160595 View on NCBI ↗
Aquilegia vestinae PV564797.1 161572 View on NCBI ↗
Aquilegia viridiflora PV564798.1 160995 View on NCBI ↗
Aquilegia vitalii PV564800.1 161923 View on NCBI ↗
Aquilegia vulgaris subsp. nevadensis PV564779.1 161368 View on NCBI ↗
Aquilegia wittmanniana PV564744.1 161513 View on NCBI ↗
Aquilegia xinjiangensis PV564801.1 161245 View on NCBI ↗
Aquilegia yabeana NC_058527.1 162094 View on NCBI ↗
Aquilegia yangii NC_058529.1 161820 View on NCBI ↗