Markers + reference

Neillia

5 species · Rosaceae · Rosales

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Species 5
Genome length 159–160 kb
Candidate markers 269
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 310 0.0270 0.95 68.4 yes View details
trnR-UCU-atpA LSC 313 0.0179 0.97 50.8 yes View details
psbZ-trnG-GCC LSC 427 0.0262 0.99 69.4 yes View details
trnT-UGU-trnL-UAA LSC 1236 0.0076 0.95 65.2 yes View details
petA-psbJ LSC 950 0.0061 1.00 51.2 yes View details
rpl20-rps12 LSC 798 0.0075 1.00 63.8 yes View details
rps19 IRb 279 0.0014 1.00 24.0 no View details
ndhF-rpl32 SSC 1095 0.0081 1.00 52.9 yes View details
rpl32-trnL-UAG SSC 931 0.0089 0.98 55.0 yes View details
ccsA SSC 966 0.0014 1.00 42.9 yes View details
ccsA-ndhD SSC 282 0.0220 1.00 61.1 yes View details
rps19 IRa 279 0.0155 0.39 39.9 yes View details
rps19-trnH-GUG LSC 71 0.0822 1.00 79.8 no View details
psbF-psbE LSC 9 0.0444 1.00 70.0 yes View details
trnM-CAU-atpE LSC 195 0.0174 1.00 65.5 yes View details
trnS-GCU-trnG-UCC LSC 657 0.0067 1.00 65.3 yes View details
trnK-UUU-rps16 LSC 918 0.0059 1.00 63.1 yes View details
ndhE-ndhG SSC 237 0.0165 1.00 62.7 yes View details
petD-rpoA LSC 251 0.0076 0.94 61.8 yes View details
atpH-atpI LSC 1153 0.0047 1.00 59.3 yes View details
rps16-trnQ-UUG LSC 627 0.0059 1.00 58.6 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 95 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 CCTCTAGACCTAGCTGCTGT 359–379 1.000 86.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 409–429 1.000 85.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 423–443 1.000 85.2
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 422–442 1.000 85.2
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 424–444 1.000 85.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 1049–1056 1.000 79.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 1048–1055 1.000 79.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 1058–1065 1.000 78.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAAAGGCGCTCAAC 1053–1060 1.000 77.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 1052–1059 1.000 77.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GCTATTCGGAGGTTCGAGTC 707–742 1.000 82.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GCTATTCGGAGGTTCGAGTC 691–726 1.000 81.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GCTATTCGGAGGTTCGAGTC 702–737 1.000 81.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GTGTCGACTAGAAATGGGGC 761–796 1.000 80.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT TATTCGGAGGTTCGAGTCCT 705–740 1.000 80.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 721–735 1.000 54.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 720–734 1.000 54.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 724–738 1.000 52.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 723–737 1.000 52.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 722–736 1.000 52.9
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 403–442 1.000 69.3
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCCCTTTTGAAAGAAGC 384–423 1.000 64.2
trnR-UCU-atpA_p3 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA AGACATTTACCGACGAAGCG 402–441 1.000 63.7
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACCAAGACATTTACCGACGA 407–446 1.000 63.4
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGAACAGATGGAACGTT 360–399 1.000 62.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1206–1211 1.000 80.6
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 1236–1241 1.000 79.7
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1207–1212 1.000 79.4
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACCTTAGCTGCG 1237–1242 1.000 78.6
atpH-atpI_p5 atpH-atpI AGGTCCAATAGAAGCAAGCC GCGAATCCATGGAAGGTCAT 1246–1251 1.000 77.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Neillia gracilis NC_072914.1 159426 View on NCBI ↗
Neillia hanceana NC_072915.1 159505 View on NCBI ↗
Neillia incisa NC_054178.1 159583 View on NCBI ↗
Neillia serratisepala NC_072916.1 159841 View on NCBI ↗
Neillia uekii NC_072917.1 159447 View on NCBI ↗