Markers + reference

Hilliella

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 154–155 kb
Candidate markers 265
Primer pairs 100

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 279 0.0903 0.99 73.8 yes View details
trnK-AAA-rps16 LSC 687 0.0312 0.98 63.8 yes View details
rps16 LSC 1161 0.0255 0.98 61.9 yes View details
trnC-UGC-petN LSC 611 0.0200 0.98 64.0 yes View details
trnE-GAA-trnT-ACC LSC 821 0.0222 0.99 64.4 yes View details
psaA-ycf3 LSC 722 0.0364 0.99 67.1 yes View details
psbE-petL LSC 1407 0.0280 0.66 66.7 yes View details
clpP LSC 2062 0.0127 0.99 51.1 yes View details
rpl16 LSC 1523 0.0218 0.99 57.2 yes View details
ycf1-rpl32 SSC 3074 0.0194 0.99 52.9 yes View details
rpl32-trnL-CUA SSC 941 0.0432 0.86 77.3 yes View details
rps12-clpP LSC 177 0.0960 1.00 87.0 yes View details
trnS-UCC-rps4 LSC 288 0.0459 0.98 80.5 yes View details
trnL-CUA-ccsA SSC 116 0.0708 0.97 76.6 yes View details
atpB-rbcL LSC 799 0.0205 0.98 72.8 yes View details
petG-trnW-UGG LSC 133 0.0391 0.96 71.4 yes View details
trnS-AGC-trnG-GGA LSC 679 0.0330 0.94 71.3 yes View details
ycf4-cemA LSC 478 0.0278 0.98 70.6 yes View details
psbB-psbT LSC 188 0.0535 0.99 69.9 yes View details
psbZ-trnG-GGC LSC 491 0.0215 0.95 69.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TGAGGCTCCATCTACAAATGG 332–336 1.000 72.9
trnH-CAC-psbA_p2 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC TGAGGCTCCATCTACAAATGG 333–337 1.000 72.6
trnH-CAC-psbA_p3 trnH-CAC-psbA AATCCACTTGGCTACATCCG TGAGGCTCCATCTACAAATGG 325–329 1.000 71.4
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTGAGGCTCCATCTACAAATGG 333–337 1.000 68.5
trnH-CAC-psbA_p5 trnH-CAC-psbA ATAACTTGGTCTCGGGCATC TGAGGCTCCATCTACAAATGG 401 0.500 42.5
trnK-AAA-rps16_p1 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1050–1072 1.000 82.0
trnK-AAA-rps16_p2 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 1051–1073 1.000 82.0
trnK-AAA-rps16_p3 trnK-AAA-rps16 TCGACACCGAAAACAAGGTT CCCAATGAGCCGTTTATCGA 1145–1165 1.000 82.0
trnK-AAA-rps16_p4 trnK-AAA-rps16 TCGACACCGAAAACAAGGTT TCCCAATGAGCCGTTTATCG 1146–1166 1.000 82.0
trnK-AAA-rps16_p5 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG CGTTTCTAGGGGGAGGGTAT 1087 0.500 59.1
rps16_p1 rps16 GTTGAGTTAGCAACCCCCAA TTTGTGTGTGATGCGGGTAA 2149 0.500 59.7
rps16_p2 rps16 CATGTGTGCGTCAGGGATAA TTTGTGTGTGATGCGGGTAA 2056 0.500 59.6
rps16_p3 rps16 TGTGCGTCAGGGATAAATGG TTTGTGTGTGATGCGGGTAA 2052 0.500 59.5
rps16_p4 rps16 GATGGAAGCGAAAGAGGAGG TTTGTGTGTGATGCGGGTAA 1531 0.500 59.3
rps16_p5 rps16 GTTGAGTTAGCAACCCCCAA GAGGTTCGAATCCTTCCGTC 2337 0.500 59.3
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AGGGGTTAAAGGAACGAATCA 738–757 1.000 68.3
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GGGGTTAAAGGAACGAATCAC 737–756 1.000 68.0
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC AGGGGTTAAAGGAACGAATCA 736–755 1.000 68.0
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC GGGGTTAAAGGAACGAATCAC 735–754 1.000 67.7
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AGGGGTTAAAGGAACGAATCAC 738–757 1.000 66.4
trnC-UGC-petN_p1 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 720–721 1.000 81.7
trnC-UGC-petN_p2 trnC-UGC-petN GTTTCTATCGTTTTGGCGGC ACTTCTTCCCCACACTACGA 776–778 1.000 81.5
trnC-UGC-petN_p3 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 721–722 1.000 81.1
trnC-UGC-petN_p4 trnC-UGC-petN GTTTCTATCGTTTTGGCGGC CACTTCTTCCCCACACTACG 777–779 1.000 80.9
trnC-UGC-petN_p5 trnC-UGC-petN TGCAAATCCCTTTTTCCCCA ACTTCTTCCCCACACTACGA 733 0.500 59.1
trnE-GAA-trnT-ACC_p1 trnE-GAA-trnT-ACC TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 952–962 1.000 81.2
trnE-GAA-trnT-ACC_p2 trnE-GAA-trnT-ACC TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 931–941 1.000 80.8
trnE-GAA-trnT-ACC_p3 trnE-GAA-trnT-ACC TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 928–938 1.000 80.6
trnE-GAA-trnT-ACC_p4 trnE-GAA-trnT-ACC GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 914–924 1.000 80.5
trnE-GAA-trnT-ACC_p5 trnE-GAA-trnT-ACC TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 893–903 1.000 80.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Hilliella fumarioides NC_061289.1 154988 View on NCBI ↗
Hilliella yixianensis NC_061287.1 154334 View on NCBI ↗