Markers + reference

Amelanchier

13 species · Rosaceae · Rosales

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Species 13
Genome length 159–160 kb
Candidate markers 269
Primer pairs 90

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 8 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-GCC-trnR-UCU LSC 220 0.0293 0.91 57.4 yes View details
trnR-UCU-atpA LSC 660 0.0233 0.90 58.1 yes View details
trnT-GGU-psbD LSC 1490 0.0065 0.92 52.2 yes View details
psbZ-trnG-UCC LSC 510 0.0152 0.85 48.3 yes View details
trnT-UGU-trnL-UAA LSC 1189 0.0075 0.96 58.6 yes View details
ndhC-trnV-UAC LSC 579 0.0155 0.94 62.8 yes View details
psaJ-rpl33 LSC 468 0.0047 1.00 47.1 yes View details
rpl33-rps18 LSC 267 0.0354 0.91 72.4 yes View details
rpl16 LSC 1390 0.0053 1.00 32.7 yes View details
rpl32-trnL-UAG SSC 1420 0.0064 0.99 45.9 yes View details
ndhF-rpl32 SSC 1089 0.0071 0.98 59.0 yes View details
petA-psbJ LSC 1002 0.0046 0.98 55.3 yes View details
atpH-atpI LSC 1179 0.0039 0.99 55.2 yes View details
rpl22-rps19 LSC 61 0.0202 1.00 53.9 yes View details
rps16-trnQ-UUG LSC 765 0.0022 1.00 52.5 yes View details
psbE-petL LSC 1232 0.0019 1.00 51.6 yes View details
petN-psbM LSC 1186 0.0029 0.98 50.2 yes View details
accD-psaI LSC 807 0.0037 0.89 50.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 688–939 1.000 82.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 698–949 1.000 80.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTT GAGGTTCGAATCCTTCCGTC 665–916 1.000 80.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 699–950 1.000 80.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTGTCGACTAGAAATGGGGC 750–1001 1.000 80.0
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 281–370 1.000 71.6
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 284–373 1.000 71.4
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 287–376 1.000 70.9
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 290–379 1.000 70.6
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 285–374 1.000 69.2
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG ACAATCTCAATCATCCCCGC 1199–1500 1.000 86.9
trnR-UCU-atpA_p2 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG ACAATCTCAATCATCCCCGC 1202–1503 1.000 86.6
trnR-UCU-atpA_p3 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TTCGGTTTCCAGGGTAGGAT 1379–1680 1.000 86.4
trnR-UCU-atpA_p4 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TCAGACCGGCCATTAATGTG 1404–1705 1.000 86.3
trnR-UCU-atpA_p5 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG TCAGACCGGCCATTAATGTG 1407–1708 1.000 86.1
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 798–1278 1.000 84.3
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 764–1244 1.000 84.2
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCAACCTTAGCTGCG 828–1308 1.000 83.4
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 794–1274 1.000 83.3
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 765–1245 1.000 83.0
petN-psbM_p1 petN-psbM AGTAAATCTCGCTTGGGCTG AAAACAGTCAGCCAAGGTGA 1271–1309 1.000 78.6
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC AAAACAGTCAGCCAAGGTGA 1214–1252 1.000 78.0
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT AAAACAGTCAGCCAAGGTGA 1213–1251 1.000 78.0
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC AAAACAGTCAGCCAAGGTGA 1212–1250 1.000 77.5
petN-psbM_p5 petN-psbM GGGGAAGGAGTGGACTCTAG AAAACAGTCAGCCAAGGTGA 1209–1247 1.000 77.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGCCAGACCAACCTACAAAA 1519–1850 1.000 84.5
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGCCAGACCAACCTACAAAA 1522–1853 1.000 84.3
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TAGGCCAGACCAACCTACAA 1521–1852 1.000 84.3
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACCTACAAAAACGAAGCGGT 1509–1840 1.000 84.3
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA TAGGCCAGACCAACCTACAA 1524–1855 1.000 84.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Amelanchier alnifolia NC_045314.1 159841 View on NCBI ↗
Amelanchier arborea NC_045313.1 159265 View on NCBI ↗
Amelanchier asiatica NC_045312.1 160438 View on NCBI ↗
Amelanchier bartramiana NC_045315.1 159749 View on NCBI ↗
Amelanchier cusickii NC_045316.1 159785 View on NCBI ↗
Amelanchier humilis NC_045317.1 159988 View on NCBI ↗
Amelanchier interior NC_045318.1 159864 View on NCBI ↗
Amelanchier obovalis MK920296.1 159973 View on NCBI ↗
Amelanchier ovalis MK920297.1 159695 View on NCBI ↗
Amelanchier pallida NC_045319.1 159838 View on NCBI ↗
Amelanchier sanguinea NC_045320.1 159916 View on NCBI ↗
Amelanchier sinica MK920291.1 159901 View on NCBI ↗
Amelanchier spicata MK920292.1 159965 View on NCBI ↗