Markers + reference

Elaeagnus

12 species · Elaeagnaceae · Rosales

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Species 12
Genome length 151–153 kb
Candidate markers 271
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 487 0.0166 0.99 56.5 yes View details
trnS-GCU-trnG-GCC LSC 506 0.0411 0.94 83.1 yes View details
atpH-atpI LSC 880 0.0196 0.95 56.1 yes View details
rpoB-trnC-GCA LSC 1170 0.0169 0.94 61.1 yes View details
trnL-UAA-trnF-GAA LSC 381 0.0265 0.75 49.1 yes View details
psaJ-rpl33 LSC 400 0.0222 0.97 61.1 yes View details
rps19 LSC 279 0.0083 1.00 31.7 yes View details
ycf1 IRb 1338 0.0041 0.94 41.8 no View details
ndhF-rpl32 SSC 1235 0.0193 0.87 61.3 yes View details
rpl32-trnL-UAG SSC 924 0.0295 0.87 66.8 yes View details
ndhA SSC 2262 0.0119 0.98 55.2 yes View details
rps15-ycf1 SSC 383 0.0275 0.97 66.9 yes View details
ycf1 SSC 5577 0.0117 0.98 48.3 yes View details
trnH-GUG-rpl2 IRb 98 0.0568 1.00 70.3 yes View details
rpl2-trnH-GUG IRa 98 0.0567 1.00 70.3 yes View details
ycf3-trnS-GGA LSC 831 0.0149 0.97 65.6 yes View details
rps8-rpl14 LSC 156 0.0129 0.96 64.4 yes View details
trnC-GCA-petN LSC 658 0.0157 0.93 63.9 yes View details
petA-psbJ LSC 376 0.0217 0.95 62.6 yes View details
trnE-UUC-trnT-GGU LSC 631 0.0177 0.97 61.5 yes View details
psbE-petL LSC 828 0.0135 0.98 61.4 yes View details
trnD-GUC-trnY-GUA LSC 378 0.0228 0.93 59.5 yes View details
rpl33-rps18 LSC 270 0.0158 1.00 59.2 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CTTGAGCCGTACGAGGAAAA 914–1057 1.000 86.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CTTGAGCCGTACGAGGAAAA 918–1061 0.917 82.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TTTTCTTGAGCCGTACGAGG 922–1065 0.917 82.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCCCGATAAGGCTCTATCCA CTTGAGCCGTACGAGGAAAA 1072–1085 0.167 50.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCCCGATAAGGCTCTATCCA TTTTCTTGAGCCGTACGAGG 1076–1089 0.167 49.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ATCAAACCGAGGACCCCTTA 601–709 1.000 91.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TAATCAAACCGAGGACCCCT 603–711 1.000 91.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ATCAAACCGAGGACCCCTTA 600–708 1.000 91.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TAATCAAACCGAGGACCCCT 602–710 1.000 91.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CAAACCGAGGACCCCTTAAC 599–707 1.000 90.5
atpH-atpI_p1 atpH-atpI TCTATTCAGCCCTCCCGTAG ATTTTTGCAACCTTAGCCGC 1318–1406 1.000 87.3
atpH-atpI_p2 atpH-atpI AAGTGCTAATGCCACAACCA CAAATTGGTCAGGGGCTCTT 1524–1615 1.000 86.5
atpH-atpI_p3 atpH-atpI TCTATTCAGCCCTCCCGTAG CAAATTGGTCAGGGGCTCTT 1683–1771 1.000 86.4
atpH-atpI_p4 atpH-atpI AAGTGCTAATGCCACAACCA TTCAAATTGGTCAGGGGCTC 1526–1617 1.000 86.4
atpH-atpI_p5 atpH-atpI TCTATTCAGCCCTCCCGTAG TTCAAATTGGTCAGGGGCTC 1685–1773 1.000 86.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCGGATTTGAACTGGGGAAA 1724–1786 1.000 86.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCTGTTTCCTACTCACGCG CCGGATTTGAACTGGGGAAA 1742–1804 1.000 86.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT AATCCCACCGTCTTCGATTG 2206–2262 0.667 73.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCTGTTTCCTACTCACGCG AATCCCACCGTCTTCGATTG 2224–2280 0.667 73.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TCTAATCCCACCGTCTTCGA 2209–2265 0.667 72.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 728–908 1.000 85.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTTGTATTGTTTGGGCGGC AGCCCAAGCGAGACTTACTA 785–965 1.000 84.8
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 789–969 1.000 83.7
trnC-GCA-petN_p4 trnC-GCA-petN CCCCTTTCCCCAGTTCAAAT AGCCCAAGCGAGACTTACTA 732–912 1.000 83.5
trnC-GCA-petN_p5 trnC-GCA-petN TTTTGTATTGTTTGGGCGGC AGAGTCCACTTCTTCCCCAT 846–1026 1.000 82.9
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 447–477 1.000 84.2
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 446–476 1.000 84.2
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 468–498 1.000 83.0
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 467–497 1.000 82.9
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GATTCTTCCTGGGTCGATGC 501–531 1.000 82.2

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
Elaeagnus angustifolia NC_040992.1 150546 View on NCBI ↗
Elaeagnus bambusetorum NC_085559.1 152265 View on NCBI ↗
Elaeagnus glabra MN306571.1 152555 View on NCBI ↗
Elaeagnus henryi NC_062127.1 152244 View on NCBI ↗
Elaeagnus loureirii MH394422.1 152204 View on NCBI ↗
Elaeagnus macrophylla NC_028066.1 152224 View on NCBI ↗
Elaeagnus macrophylla x Elaeagnus pungens OM935758.1 152284 View on NCBI ↗
Elaeagnus mollis NC_036932.1 151428 View on NCBI ↗
Elaeagnus multiflora LC522136.1 152267 View on NCBI ↗
Elaeagnus oldhamii NC_081911.1 152283 View on NCBI ↗
Elaeagnus pungens NC_058887.1 152218 View on NCBI ↗
Elaeagnus umbellata MN599114.1 152206 View on NCBI ↗