Markers + reference

Alangium

6 species · Cornaceae · Cornales

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Species 6
Genome length 157–157 kb
Candidate markers 271
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 394 0.0220 1.00 59.2 yes View details
trnK-UUU-rps16 LSC 749 0.0070 1.00 54.3 yes View details
trnS-GCU-trnG-UCC LSC 739 0.0060 1.00 48.0 yes View details
trnC-GCA-petN LSC 583 0.0064 1.00 44.2 yes View details
trnF-GAA-ndhJ LSC 687 0.0065 1.00 48.8 yes View details
petA-psbJ LSC 1030 0.0086 1.00 51.2 yes View details
rrn16-trnI-GAU IRb 295 0.0174 1.00 38.9 yes View details
ycf1 IRb 1052 0.0015 1.00 32.4 no View details
ndhF-rpl32 SSC 1200 0.0072 1.00 52.5 yes View details
ndhD SSC 1530 0.0025 1.00 47.0 yes View details
ycf1 SSC 5472 0.0043 1.00 32.0 yes View details
ycf1-ndhF SSC 23 0.0725 1.00 58.4 yes View details
ndhD-psaC SSC 100 0.0480 1.00 57.1 yes View details
ndhA SSC 2207 0.0028 1.00 53.6 yes View details
trnL-UAA-trnF-GAA LSC 348 0.0079 1.00 53.0 yes View details
rpl20-rps12 LSC 789 0.0021 1.00 52.6 yes View details
ycf3-trnS-GGA LSC 822 0.0045 1.00 51.3 yes View details
rpl32-trnL-UAG SSC 915 0.0039 1.00 50.6 yes View details
trnE-UUC-trnT-GGU LSC 797 0.0030 1.00 49.4 yes View details
rpl16 LSC 1436 0.0034 1.00 49.3 yes View details
rps4-trnT-UGU LSC 370 0.0056 1.00 49.2 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 105 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 TTCCCTCTAGACCTAGCTGC 462–469 1.000 82.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 476–483 1.000 82.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 475–482 1.000 82.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 477–484 1.000 82.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 511–518 1.000 80.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 GTCGTGGTCTTCCAAACCTT CCTTGAAAAAGGCGCTCAAC 958–959 1.000 79.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGTGGTCTTCCAAACCTT CTTGAAAAAGGCGCTCAACC 957–958 1.000 79.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGAATTCCTCGCTTCATCCA CCTTGAAAAAGGCGCTCAAC 924–925 1.000 78.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGAATTCCTCGCTTCATCCA CTTGAAAAAGGCGCTCAACC 923–924 1.000 78.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGTGGTCTTCCAAACCTT ACTTCCTTGAAAAAGGCGCT 962–963 1.000 78.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAATCAAACCAAAAGACCCCT 852–856 1.000 64.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAATCAAACCAAAAGACCCCT 851–855 1.000 64.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATCAAACCAAAAGACCCCT 906–910 1.000 63.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAATCAAACCAAAAGACCCC 852–856 1.000 62.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAATCAAACCAAAAGACCCC 851–855 1.000 62.2
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGCCCAAGCCAGACTTACTA 705–706 1.000 80.3
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCCAGACTTACTA 649–650 1.000 80.2
trnC-GCA-petN_p3 trnC-GCA-petN GGTGTCGCCTGATCAAGAAA AGCCCAAGCCAGACTTACTA 630–631 1.000 79.4
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCCAGACTTACTA 667–668 1.000 78.0
trnC-GCA-petN_p5 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGAGTCCACTTCTTCCCCAT 766–767 1.000 77.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 938–947 1.000 79.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 917–926 1.000 79.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 914–923 1.000 79.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 900–909 1.000 78.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 879–888 1.000 78.8
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA GGTGAATTAGGTGACGGTCC 1024–1033 1.000 67.9
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA GGTGAATTAGGTGACGGTCC 1025–1034 1.000 67.9
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA CCCTCGGTAAACAAAAGCCT 985–994 1.000 67.4
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA CCCTCGGTAAACAAAAGCCT 986–995 1.000 67.4
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA TTCCAATGCTACGCCTTGAA 956–965 1.000 66.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Alangium alpinum MG525003.1 156673 View on NCBI ↗
Alangium chinense NC_044840.1 156656 View on NCBI ↗
Alangium chinense subsp. pauciflorum OR197701.1 156670 View on NCBI ↗
Alangium chinense subsp. strigosum OR197702.1 156672 View on NCBI ↗
Alangium kurzii NC_044826.1 156868 View on NCBI ↗
Alangium platanifolium NC_044827.1 156781 View on NCBI ↗