Markers + reference

Acorus

4 species · Acoraceae · Acorales

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Species 4
Genome length 153–154 kb
Candidate markers 268
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 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNA-His (GUG)-psbA LSC 385 0.0652 0.35 57.5 yes View details
tRNA-Thr (GGU)-psbD LSC 1365 0.0150 1.00 64.5 yes View details
ycf3-tRNA-Ser (GGA) LSC 828 0.0127 0.99 52.1 yes View details
ndhC-tRNA-Val (UAC) LSC 1912 0.0109 1.00 49.3 yes View details
atpE LSC 405 0.0140 1.00 39.8 yes View details
rbcL-psaI LSC 1259 0.0116 1.00 52.2 yes View details
petA-psbJ LSC 878 0.0192 1.00 57.0 yes View details
ndhF SSC 2220 0.0089 1.00 49.7 yes View details
ndhF-rpl32 SSC 851 0.0170 0.96 63.1 yes View details
rpl32-tRNA-Leu (UAG) SSC 863 0.0145 0.98 61.1 yes View details
ycf1 SSC 5742 0.0098 0.99 36.7 yes View details
tRNA-Cys (GCA)-petN LSC 880 0.0100 1.00 68.6 yes View details
rpl2-tRNA-His (GUG) IRa 31 0.0000 0.99 67.7 no View details
psbT-psbN LSC 59 0.0452 1.00 64.7 yes View details
ccsA-ndhD SSC 227 0.0323 1.00 63.2 yes View details
tRNA-Lys (UUU)-rps16 LSC 694 0.0108 1.00 60.0 yes View details
tRNA-Met (CAU)-atpE LSC 165 0.0434 1.00 58.1 yes View details
matK-tRNA-Lys (UUU) LSC 707 0.0087 1.00 55.1 yes View details
psaA-ycf3 LSC 618 0.0113 0.99 55.1 yes View details
ycf1-tRNA-Asn (GUU) IRa 603 0.0058 0.79 55.0 yes View details
rpl16 LSC 1347 0.0095 1.00 54.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
tRNA-His (GUG)-psbA_p1 tRNA-His (GUG)-psbA CTGCCTTAATCCACTTGGCT TAATATCGTCGCTGCTCACG 742 0.250 48.7
tRNA-His (GUG)-psbA_p2 tRNA-His (GUG)-psbA CTGCCTTAATCCACTTGGCT TCCATTCCACATGTTAGGCG 895 0.250 48.6
tRNA-His (GUG)-psbA_p3 tRNA-His (GUG)-psbA ACTGCCTTAATCCACTTGGC TAATATCGTCGCTGCTCACG 743 0.250 48.5
tRNA-His (GUG)-psbA_p4 tRNA-His (GUG)-psbA ACTGCCTTAATCCACTTGGC TCCATTCCACATGTTAGGCG 896 0.250 48.4
tRNA-His (GUG)-psbA_p5 tRNA-His (GUG)-psbA CTGCCTTAATCCACTTGGCT GTTGACAGTCAAGGTCGTGT 561 0.250 48.4
matK-tRNA-Lys (UUU)_p1 matK-tRNA-Lys (UUU) AGTGCGTAGATGTACTCCTGA TCTGGGTTGCTAACTCAACG 839 1.000 71.6
matK-tRNA-Lys (UUU)_p2 matK-tRNA-Lys (UUU) AGTGCGTAGATGTACTCCTGA AACGGTAGAGTACTCGGCTT 823 1.000 71.6
matK-tRNA-Lys (UUU)_p3 matK-tRNA-Lys (UUU) AGTGCGTAGATGTACTCCTGA ACGGTAGAGTACTCGGCTTT 822 1.000 71.6
matK-tRNA-Lys (UUU)_p4 matK-tRNA-Lys (UUU) GACGAGACCCATCTTTTTCGA TCTGGGTTGCTAACTCAACG 790 1.000 71.3
matK-tRNA-Lys (UUU)_p5 matK-tRNA-Lys (UUU) GACGAGACCCATCTTTTTCGA ACGGTAGAGTACTCGGCTTT 773 1.000 71.3
tRNA-Lys (UUU)-rps16_p1 tRNA-Lys (UUU)-rps16 AAAGCCGAGTACTCTACCGT TTTTCTGGAAAAGGGGGCTC 825–839 1.000 80.1
tRNA-Lys (UUU)-rps16_p2 tRNA-Lys (UUU)-rps16 AAGCCGAGTACTCTACCGTT TTTTCTGGAAAAGGGGGCTC 824–838 1.000 80.1
tRNA-Lys (UUU)-rps16_p3 tRNA-Lys (UUU)-rps16 CCGCACTTAAAAGCCGAGTA TTTTCTGGAAAAGGGGGCTC 834–848 1.000 79.2
tRNA-Lys (UUU)-rps16_p4 tRNA-Lys (UUU)-rps16 AAAGCCGAGTACTCTACCGT GAAAAGGGGGCTCAACCTAC 818–832 1.000 78.9
tRNA-Lys (UUU)-rps16_p5 tRNA-Lys (UUU)-rps16 AAGCCGAGTACTCTACCGTT GAAAAGGGGGCTCAACCTAC 817–831 1.000 78.9
tRNA-Cys (GCA)-petN_p1 tRNA-Cys (GCA)-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 768–967 1.000 84.5
tRNA-Cys (GCA)-petN_p2 tRNA-Cys (GCA)-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACA 762–961 1.000 83.8
tRNA-Cys (GCA)-petN_p3 tRNA-Cys (GCA)-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 786–985 1.000 82.3
tRNA-Cys (GCA)-petN_p4 tRNA-Cys (GCA)-petN TGTATTGTTTTGGCGGCATG TTAAAGCAGCCCAAGCAAGA 821–1020 1.000 82.2
tRNA-Cys (GCA)-petN_p5 tRNA-Cys (GCA)-petN GTATTGTTTTGGCGGCATGG TTAAAGCAGCCCAAGCAAGA 820–1019 1.000 82.2
tRNA-Thr (GGU)-psbD_p1 tRNA-Thr (GGU)-psbD GTGGTAGAGTAACGCCATGG TCCGTAACCAGTCGTCCATA 1479–1528 1.000 81.7
tRNA-Thr (GGU)-psbD_p2 tRNA-Thr (GGU)-psbD TCAGTGGTAGAGTAACGCCA TCCGTAACCAGTCGTCCATA 1482–1531 1.000 81.5
tRNA-Thr (GGU)-psbD_p3 tRNA-Thr (GGU)-psbD GTGGTAGAGTAACGCCATGG GAAGAGCAATAGACCGGACC 1523–1572 1.000 80.8
tRNA-Thr (GGU)-psbD_p4 tRNA-Thr (GGU)-psbD GTGGTAGAGTAACGCCATGG GGAAGAGCAATAGACCGGAC 1524–1573 1.000 80.8
tRNA-Thr (GGU)-psbD_p5 tRNA-Thr (GGU)-psbD TCAGTGGTAGAGTAACGCCA GAAGAGCAATAGACCGGACC 1526–1575 1.000 80.6
psaA-ycf3_p1 psaA-ycf3 GTTCTTGAAAAATGGCCGGG AGCGCAGAATTGGTTGAAGA 757–762 1.000 80.3
psaA-ycf3_p2 psaA-ycf3 GTTCTTGAAAAATGGCCGGG TGAAGATCACAAGGCGGTTC 743–748 1.000 79.7
psaA-ycf3_p3 psaA-ycf3 CCCATGCCTCGAAAGAAGTT AGCGCAGAATTGGTTGAAGA 732–737 1.000 79.6
psaA-ycf3_p4 psaA-ycf3 GTTCTTGAAAAATGGCCGGG TTGAAGATCACAAGGCGGTT 744–749 1.000 79.0
psaA-ycf3_p5 psaA-ycf3 CCCATGCCTCGAAAGAAGTT TGAAGATCACAAGGCGGTTC 718–723 1.000 79.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Acorus calamus NC_007407.1 153821 View on NCBI ↗
Acorus calamus var. americanus NC_010093.1 153819 View on NCBI ↗
Acorus gramineus NC_026299.1 152849 View on NCBI ↗
Acorus shannai PQ456444.1 153515 View on NCBI ↗