Markers + reference

Alchemilla

12 species · Rosaceae · Rosales

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Species 12
Genome length 151–152 kb
Candidate markers 275
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 707 0.0501 0.98 80.6 yes View details
rps16-trnQ-UUG LSC 671 0.0455 0.97 83.3 yes View details
trnR-UCU-atpA LSC 662 0.0549 0.88 79.9 yes View details
petN-psbM LSC 1234 0.0392 0.97 76.2 yes View details
psbZ-trnG-GCC LSC 323 0.0348 0.94 72.8 yes View details
trnT-UGU-trnL-UAA LSC 697 0.0391 0.97 82.9 yes View details
trnL-UAA-trnF-GAA LSC 391 0.0423 1.00 76.2 yes View details
ndhC-trnV-UAC LSC 579 0.0508 0.92 83.4 yes View details
ndhF SSC 2232 0.0183 1.00 52.6 yes View details
ndhF-rpl32 SSC 607 0.0420 0.94 80.5 yes View details
rpl32-trnL-UAG SSC 667 0.0435 0.97 78.1 yes View details
petA-psbJ LSC 931 0.0357 0.90 80.4 yes View details
trnT-GGU-psbD LSC 1278 0.0313 0.99 80.3 yes View details
trnF-GAA-ndhJ LSC 546 0.0395 0.99 80.1 yes View details
trnH-GUG-psbA LSC 188 0.0660 0.99 79.4 yes View details
atpF-atpH LSC 496 0.0333 0.95 79.3 yes View details
trnG-GCC-trnfM-CAU LSC 189 0.0743 1.00 75.9 yes View details
ycf3-trnS-GGA LSC 455 0.0364 1.00 75.7 yes View details
rps2-rpoC2 LSC 210 0.0551 0.99 75.3 yes View details
trnS-GCU-trnG-UCC LSC 344 0.0353 1.00 75.1 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 GATCCACTTGGCTACATCCG ACCGCGCTAATCTTGGTATG 296–309 1.000 89.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ACCGCGCTAATCTTGGTATG 310–323 1.000 89.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC ACCGCGCTAATCTTGGTATG 309–322 1.000 89.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC ACCGCGCTAATCTTGGTATG 311–324 1.000 89.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGCGCTAATCTTGGTATGGA 294–307 1.000 89.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 710–998 1.000 91.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGAGATCTTCGGAAAGTGGG 792–1080 1.000 91.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAGTGGTATGTTGCTGCCA 1472–1592 0.917 87.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAAGTGGTATGTTGCTGCCA 1468–1588 0.917 86.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT AAAGTGGTATGTTGCTGCCA 1469–1589 0.917 86.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 730–763 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 741–774 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 734–767 1.000 85.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 760–793 1.000 85.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 742–775 1.000 85.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AGTAATCAAACCGAAAGACCCT 446–460 1.000 69.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGTAATCAAACCGAAAGACCCT 447–461 1.000 68.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AATCAAACCGAAAGACCCTT 444–458 1.000 67.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATCAAACCGAAAGACCCTTT 443–457 1.000 67.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AGTAATCAAACCGAAAGACCCT 501–515 1.000 66.7
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGACCAAATGGAACGTT 636–783 1.000 73.3
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAGGACCAAATGGAACGT 637–784 1.000 73.3
trnR-UCU-atpA_p3 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TCAGGACCAAATGGAACGTT 671–818 1.000 70.4
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TTCAGGACCAAATGGAACGT 672–819 1.000 70.4
trnR-UCU-atpA_p5 trnR-UCU-atpA GGAGTAAAAAGCGTCCATTGTC TCAGGACCAAATGGAACGTT 696–843 0.917 66.8
atpF-atpH_p1 atpF-atpH GATGGCCAATAACCCAAGGA CCAGAGGCGGAAGGAAAAAT 623–701 1.000 84.4
atpF-atpH_p2 atpF-atpH GGATGGCCAATAACCCAAGG CCAGAGGCGGAAGGAAAAAT 624–702 1.000 83.3
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG CCAGAGGCGGAAGGAAAAAT 645–723 0.917 83.2
atpF-atpH_p4 atpF-atpH TGGCCAATAACCCAAGGAAA CCAGAGGCGGAAGGAAAAAT 621–699 1.000 82.4
atpF-atpH_p5 atpF-atpH ATGGCCAATAACCCAAGGAA CCAGAGGCGGAAGGAAAAAT 622–700 1.000 80.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Alchemilla argyrophylla NC_049037.1 152427 View on NCBI ↗
Alchemilla exigua PP316508.1 151947 View on NCBI ↗
Alchemilla glaucescens PP316509.1 151906 View on NCBI ↗
Alchemilla guatemalensis NC_087026.1 152014 View on NCBI ↗
Alchemilla holosericea NC_087027.1 152075 View on NCBI ↗
Alchemilla microcarpa NC_087047.1 150586 View on NCBI ↗
Alchemilla monticola PP316510.1 151881 View on NCBI ↗
Alchemilla orbiculata NC_087025.1 151877 View on NCBI ↗
Alchemilla pedata NC_049038.1 152438 View on NCBI ↗
Alchemilla transiens PP316511.1 152275 View on NCBI ↗
Alchemilla vetteri PX223350.1 151924 View on NCBI ↗
Alchemilla vulcanica NC_087024.1 152022 View on NCBI ↗