Markers + reference

Alnus

38 species · Betulaceae · Fagales

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Species 38
Genome length 160–161 kb
Candidate markers 278
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 10 remaining regions by MarkerSeek score (out of 278 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 434 0.0278 0.98 65.0 yes View details
trnK-UUU-rps16 LSC 1039 0.0161 0.99 65.8 yes View details
trnS-GCU-trnG-UCC LSC 1025 0.0253 0.91 72.5 yes View details
trnF-GAA-ndhJ LSC 816 0.0230 0.93 65.2 yes View details
accD-psaI LSC 934 0.0158 0.96 70.6 yes View details
ycf1 IRb 1204 0.0008 1.00 35.6 no View details
ndhF SSC 2256 0.0082 1.00 46.4 yes View details
rpl32-trnL-UAG SSC 1313 0.0176 0.98 61.3 yes View details
ndhA SSC 2250 0.0071 1.00 45.2 yes View details
ycf1 SSC 5769 0.0080 1.00 38.7 yes View details
rpl2-trnH-GUG IRa 32 0.0434 1.00 66.8 no View details
trnT-UGU-trnL-UAA LSC 900 0.0112 0.98 65.2 yes View details
ycf1-ndhF SSC 72 0.1235 1.00 64.4 yes View details
atpH-atpI LSC 1278 0.0088 0.99 63.2 yes View details
ycf4-cemA LSC 416 0.0095 0.99 60.5 yes View details
ycf3-trnS-GGA LSC 426 0.0201 1.00 60.3 yes View details
trnL-UAG-ccsA SSC 107 0.0189 0.99 60.3 yes View details
rps15-ycf1 SSC 453 0.0144 0.98 59.1 yes View details
trnE-UUC-trnT-GGU LSC 955 0.0114 1.00 58.0 yes View details
rps16-trnQ-UUG LSC 1478 0.0112 1.00 57.7 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-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 247–611 1.000 88.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 261–625 1.000 87.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 260–624 1.000 87.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 262–626 1.000 87.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 248–612 1.000 87.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCAAAGAAGGCGGGAGTTTT 943–1179 1.000 85.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCAAAGAAGGCGGGAGTTT 944–1180 1.000 85.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAAAGAAGGCGGGAGTTTT 942–1178 1.000 85.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCAAAGAAGGCGGGAGTTT 943–1179 1.000 85.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCAAAGAAGGCGGGAGTT 944–1180 1.000 85.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CACAGCCGACCATATCCTTC GGTATTCGGAGGTTCGACTC 1573–1628 1.000 80.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGTATTCGGAGGTTCGACTC 1553–1608 1.000 80.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CACAGCCGACCATATCCTTC GGGTTTTGGTCCCGGTATTC 1586–1641 1.000 80.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 1566–1621 1.000 80.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CACAGCCGACCATATCCTTC TAAGGCAACGGGTTTTGGTC 1595–1650 1.000 79.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 777–1131 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 776–1130 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACAAAAGCGGAAAGAGAGGG ACGAATCACACTTTTACCACT 837–1191 1.000 62.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 780–1134 1.000 62.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 779–1133 1.000 62.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1316–1399 1.000 85.4
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGGC TTTTGCAACTTTAGCTGCGG 1401–1484 1.000 85.0
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1317–1400 1.000 84.2
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT AGGCGAATCTATGGAGGGTT 1337–1338 0.053 40.4
atpH-atpI_p5 atpH-atpI GATCCCTTCTACAGCTTGGC AGGCGAATCTATGGAGGGTT 1422–1423 0.053 40.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 779–1121 1.000 85.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 758–1100 1.000 85.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 758–1100 1.000 85.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 737–1079 1.000 85.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 755–1097 1.000 85.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (38)

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

Species Accession Length (bp) Link
Alnus acuminata OL891508.1 160666 View on NCBI ↗
Alnus alnobetula subsp. alnobetula MT872517.1 160502 View on NCBI ↗
Alnus alnobetula subsp. crispa OL891505.1 160532 View on NCBI ↗
Alnus alnobetula subsp. fruticosa OL891503.1 160134 View on NCBI ↗
Alnus alnobetula subsp. mandschurica OL891504.1 160556 View on NCBI ↗
Alnus alnobetula subsp. maximowiczii NC_036754.1 160586 View on NCBI ↗
Alnus alnobetula subsp. suaveolens MF136496.1 160570 View on NCBI ↗
Alnus cordata NC_036751.1 160847 View on NCBI ↗
Alnus fauriei OL891518.1 160934 View on NCBI ↗
Alnus ferdinandi-coburgii OL891514.1 161108 View on NCBI ↗
Alnus firma OL891506.1 160013 View on NCBI ↗
Alnus formosana NC_061930.1 161029 View on NCBI ↗
Alnus glutinosa NC_039930.1 160770 View on NCBI ↗
Alnus glutinosa subsp. barbata MF136501.1 160916 View on NCBI ↗
Alnus glutinosa subsp. betuloides MF136499.1 160774 View on NCBI ↗
Alnus glutinosa subsp. glutinosa MF136502.1 160827 View on NCBI ↗
Alnus hirsuta PX512379.1 160879 View on NCBI ↗
Alnus hirsuta var. sibirica OL891511.1 160902 View on NCBI ↗
Alnus incana NC_036752.1 160807 View on NCBI ↗
Alnus incana subsp. tenuifolia OL891509.1 160688 View on NCBI ↗
Alnus japonica NC_036753.1 160788 View on NCBI ↗
Alnus jorullensis subsp. jorullensis MF136508.1 160617 View on NCBI ↗
Alnus lanata OL891517.1 161117 View on NCBI ↗
Alnus maritima OL891520.1 160577 View on NCBI ↗
Alnus maritima subsp. maritima MF136509.1 160547 View on NCBI ↗
Alnus maritima subsp. oklahomensis MF136511.1 160586 View on NCBI ↗
Alnus matsumurae OL891510.1 160914 View on NCBI ↗
Alnus nepalensis NC_039991.1 160735 View on NCBI ↗
Alnus nitida NC_036755.1 160871 View on NCBI ↗
Alnus orientalis NC_036756.1 160470 View on NCBI ↗
Alnus pendula OL891507.1 160626 View on NCBI ↗
Alnus rhombifolia OL891512.1 160729 View on NCBI ↗
Alnus rubra NC_036757.1 160754 View on NCBI ↗
Alnus serrulata OL891515.1 160522 View on NCBI ↗
Alnus serrulatoides OL891519.1 160864 View on NCBI ↗
Alnus subcordata NC_036758.1 160702 View on NCBI ↗
Alnus trabeculosa OL891513.1 160744 View on NCBI ↗
Alnus x mayrii OL891516.1 160758 View on NCBI ↗