Markers + reference

Argentina

15 species · Rosaceae · Rosales

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Species 15
Genome length 155–157 kb
Candidate markers 265
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 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 355 0.1046 0.87 78.0 yes View details
trnK-UUU-rps16 LSC 816 0.0419 0.84 75.2 yes View details
rps16-trnQ-UUG LSC 983 0.0563 0.98 89.4 yes View details
trnQ-UUG-psbK LSC 414 0.0416 0.96 81.9 yes View details
trnR-UCU-atpA LSC 543 0.0601 0.94 83.8 yes View details
atpH-atpI LSC 938 0.0466 0.97 83.7 yes View details
petN-psbM LSC 935 0.0388 0.96 81.3 yes View details
psbZ-trnG-GCC LSC 353 0.0437 0.94 73.4 yes View details
trnT-UGU-trnL-UAA LSC 1050 0.0478 0.94 84.7 yes View details
ndhF-rpl32 SSC 1143 0.0571 0.95 85.5 yes View details
trnF-GAA-ndhJ LSC 732 0.0335 0.96 85.4 yes View details
rpl32-trnL-UAG SSC 713 0.0415 0.94 84.8 yes View details
rpl14-rpl16 LSC 136 0.0523 0.99 84.0 yes View details
rpl2-trnH IRa 62 0.0696 0.99 83.8 no View details
accD-psaI LSC 429 0.0528 1.00 82.4 yes View details
trnS-GGA-trnG-UCC LSC 554 0.0382 0.95 81.0 yes View details
trnG-GCC-trnfM-CAU LSC 210 0.0590 0.99 80.2 yes View details
trnT-GGU-psbD LSC 1232 0.0279 0.98 80.1 yes View details
rpl36-rps8 LSC 497 0.0386 0.98 80.1 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 289–452 1.000 90.4
trnH-psbA_p2 trnH-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 339–502 0.933 88.0
trnH-psbA_p3 trnH-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 353–516 0.933 88.0
trnH-psbA_p4 trnH-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 352–515 0.933 88.0
trnH-psbA_p5 trnH-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 354–517 0.933 88.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 889–1088 1.000 91.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGACGAGAGGGAAGAGATCT 983–1182 1.000 91.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CAGCGGAAAAGCTTTTACCG AAAAAGGCGCTCAACCTACA 1238–1373 0.467 68.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGCGGAAAAGCTTTTACCG CGACGAGAGGGAAGAGATCT 1332–1467 0.467 68.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAACGGGCTCTCTCTCTCTA AAAAAGGCGCTCAACCTACA 1577–1627 0.133 46.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1009–1204 1.000 91.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1007–1202 1.000 91.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 991–1186 0.933 87.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GATGTAAGACTCCACAGCGG GAGGTTCGAATCCTTCCGTC 1023–1218 0.867 85.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATGTAAGACTCCACAGCG GAGGTTCGAATCCTTCCGTC 1024–1219 0.867 85.5
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GGGCAATTTGGCTACGAAAA 523–581 1.000 80.7
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GAATAGCGGGACCAAAACCC GGGCAATTTGGCTACGAAAA 532–590 1.000 78.9
trnQ-UUG-psbK_p3 trnQ-UUG-psbK AAAACCCGTTGCCTTACCAC GGGCAATTTGGCTACGAAAA 519–577 1.000 78.4
trnQ-UUG-psbK_p4 trnQ-UUG-psbK ACCAAAACCCGTTGCCTTAC GGGCAATTTGGCTACGAAAA 522–580 1.000 78.4
trnQ-UUG-psbK_p5 trnQ-UUG-psbK CAAAACCCGTTGCCTTACCA GGGCAATTTGGCTACGAAAA 520–578 1.000 78.4
trnS-GGA-trnG-UCC_p1 trnS-GGA-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 592–636 1.000 63.7
trnS-GGA-trnG-UCC_p2 trnS-GGA-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 591–635 1.000 63.7
trnS-GGA-trnG-UCC_p3 trnS-GGA-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 595–639 1.000 62.6
trnS-GGA-trnG-UCC_p4 trnS-GGA-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 594–638 1.000 62.6
trnS-GGA-trnG-UCC_p5 trnS-GGA-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 593–637 1.000 62.6
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACGTTTTCTACTTCAGGA 597–740 1.000 57.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACGTTTTCTACTTCAGGAA 597–740 1.000 54.2
trnR-UCU-atpA_p3 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TGGAACGTTTTCTACTTCAGGA 632–775 1.000 54.2
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGGAACGTTTTCTACTTCAGG 597–740 1.000 53.2
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ATGGAACGTTTTCTACTTCAGGA 598–741 1.000 52.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Argentina anserina NC_060513.1 155659 View on NCBI ↗
Argentina cardotiana NC_086976.1 156798 View on NCBI ↗
Argentina festiva OR863691.1 156980 View on NCBI ↗
Argentina gombalana NC_086978.1 156059 View on NCBI ↗
Argentina leuconota PX057650.1 155709 View on NCBI ↗
Argentina leuconota var. brachyphyllaria OR863692.1 155621 View on NCBI ↗
Argentina leuconota var. leuconota OR863694.1 155452 View on NCBI ↗
Argentina parvula OR863707.1 156318 View on NCBI ↗
Argentina peduncularis NC_086979.1 155650 View on NCBI ↗
Argentina phanerophlebia NC_050936.1 155565 View on NCBI ↗
Argentina polyphylla NC_086985.1 156720 View on NCBI ↗
Argentina smithiana NC_086981.1 156753 View on NCBI ↗
Argentina stenophylla NC_086982.1 156007 View on NCBI ↗
Argentina stenophylla var. emergens PP234515.1 155136 View on NCBI ↗
Argentina taliensis NC_086984.1 156523 View on NCBI ↗