Markers + reference

Hippophae

13 species · Elaeagnaceae · Rosales

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Species 13
Genome length 155–156 kb
Candidate markers 275
Primer pairs 95

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
rps16-trnQ-UUG LSC 1439 0.0172 1.00 69.5 yes View details
trnR-UCU-atpA LSC 249 0.0227 0.99 66.8 yes View details
rpoB-trnC-GCA LSC 1274 0.0326 0.99 78.1 yes View details
trnC-GCA-petN LSC 831 0.0228 0.99 72.1 yes View details
psbZ-trnG-UCC LSC 542 0.0275 1.00 79.4 yes View details
rps4-trnT-UGU LSC 675 0.0230 1.00 71.3 yes View details
ycf1 IRb 1269 0.0026 1.00 37.2 no View details
ndhF-rpl32 SSC 1270 0.0265 1.00 75.2 yes View details
rpl32-trnL-UAG SSC 1182 0.0290 1.00 74.6 yes View details
ycf1 SSC 5658 0.0107 1.00 52.8 yes View details
trnR-ACG-rrn5 IRa 252 0.0522 1.00 81.7 yes View details
rrn5-trnR-ACG IRb 252 0.0526 1.00 81.7 yes View details
trnG-GCC-trnR-UCU LSC 201 0.0408 1.00 77.3 yes View details
rbcL-accD LSC 928 0.0155 0.98 75.6 yes View details
rps8-rpl14 LSC 178 0.0290 1.00 72.0 yes View details
petN-psbM LSC 550 0.0227 1.00 71.8 yes View details
trnT-UGU-trnL-UAA LSC 796 0.0179 0.99 71.6 yes View details
trnE-UUC-trnT-GGU LSC 678 0.0182 1.00 70.9 yes View details
trnS-GCU-trnG-GCC LSC 716 0.0167 0.99 70.4 yes View details
tRNA-GUC-trnY-GUA LSC 320 0.0254 1.00 69.9 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCGAACATCAATTGCAACGA GAGGTTCGAATCCTTCCGTC 1366–1549 1.000 76.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCGAACATCAATTGCAACGA TAAGGCATCGGGTTTTGGTC 1396–1579 1.000 75.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GATCGAACATCAATTGCAACGA GAGGTTCGAATCCTTCCGTC 1368–1551 1.000 73.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCGAACATCAATTGCAACGA GTAAGGCATCGGGTTTTGGT 1397–1580 1.000 73.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCGAACATCAATTGCAACGA GTGGTAAGGCATCGGGTTTT 1400–1583 1.000 73.1
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ATCAAACCGAGGACCCCTTA 664–825 1.000 88.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TAATCAAACCGAGGACCCCT 666–827 1.000 88.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ATCAAACCGAGGACCCCTTA 663–824 1.000 88.8
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TAATCAAACCGAGGACCCCT 665–826 1.000 88.8
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CAAACCGAGGACCCCTTAAC 662–823 1.000 87.7
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 275–301 1.000 72.7
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 278–304 1.000 72.5
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 281–307 1.000 72.0
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 284–310 1.000 71.8
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 279–305 1.000 70.3
trnR-UCU-atpA_p1 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGCACTTTTGAAAGAGGCGA 383–401 1.000 76.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGCACTTTTGAAAGAGGCGA 323–341 1.000 75.7
trnR-UCU-atpA_p3 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT CATTTACGGGGGAAGCAGAA 402–420 1.000 75.1
trnR-UCU-atpA_p4 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AAGACATTTACGGGGGAAGC 406–424 1.000 75.1
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTTACGGGGGAAGCAGAA 342–360 1.000 74.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCATTCCCACCTCCAAGCAT CCGGATTTGAACTGGGGAAA 1263–1359 1.000 83.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCATTCCCACCTCCAAGCAT AAAGAGGATTTGCAGTCCCC 1245–1341 1.000 82.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTCATTCCCACCTCCAAGCA CCGGATTTGAACTGGGGAAA 1264–1360 1.000 81.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCATTCCCACCTCCAAGCA AAAGAGGATTTGCAGTCCCC 1246–1342 1.000 80.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCATTCCCACCTCCAAGCA CCGGATTTGAACTGGGGAAA 1263–1359 1.000 78.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 781–983 1.000 90.0
trnC-GCA-petN_p2 trnC-GCA-petN GGGGACTGCAAATCCTCTTT AGCCCAAGCGAGACTTACTA 799–1001 1.000 88.7
trnC-GCA-petN_p3 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 838–958 0.923 85.7
trnC-GCA-petN_p4 trnC-GCA-petN TGCAAATCCTCTTTTCCCCA AGCCCAAGCGAGACTTACTA 793–995 1.000 85.0
trnC-GCA-petN_p5 trnC-GCA-petN GGTGTCGCCTGATCAACAAA AGCCCAAGCGAGACTTACTA 762–964 0.923 80.7

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
Hippophae goniocarpa MW791524.1 156312 View on NCBI ↗
Hippophae gyantsensis NC_044478.1 155260 View on NCBI ↗
Hippophae neurocarpa NC_047483.1 156316 View on NCBI ↗
Hippophae neurocarpa subsp. neurocarpa MT512453.1 154995 View on NCBI ↗
Hippophae rhamnoides NC_035548.1 156132 View on NCBI ↗
Hippophae rhamnoides subsp. caucasica NC_083090.1 156185 View on NCBI ↗
Hippophae rhamnoides subsp. mongolica NC_083089.1 156404 View on NCBI ↗
Hippophae rhamnoides subsp. rhamnoides MT512450.1 156111 View on NCBI ↗
Hippophae rhamnoides subsp. sinensis NC_049156.1 156355 View on NCBI ↗
Hippophae rhamnoides subsp. turkestanica PV850015.1 156101 View on NCBI ↗
Hippophae rhamnoides subsp. yunnanensis NC_044479.1 156415 View on NCBI ↗
Hippophae salicifolia NC_056188.1 155420 View on NCBI ↗
Hippophae tibetana NC_062882.1 155804 View on NCBI ↗