Markers + reference

Himalayacalamus

2 species · Poaceae · Poales

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Species 2
Genome length 140–140 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

10 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
trnK-UUU-rps16 LSC 556 0.0054 1.00 60.9 yes View details
trnS-GCU-psbD LSC 981 0.0031 1.00 48.8 yes View details
trnG-UCC-trnT-GGU LSC 1889 0.0032 1.00 52.8 yes View details
trnC-GCA-rpoB LSC 1178 0.0034 1.00 60.7 yes View details
rpoC2 LSC 4554 0.0015 1.00 50.6 yes View details
ycf3-trnS-GGA LSC 593 0.0622 0.98 91.0 yes View details
trnL-UAA-trnF-GAA LSC 346 0.0116 1.00 60.1 yes View details
psbE-petL LSC 1228 0.0065 1.00 62.5 yes View details
psaJ-rpl33 LSC 450 0.0044 1.00 58.2 yes View details
ndhG SSC 531 0.0019 1.00 50.5 yes View details
rps19-psbA LSC 128 0.0234 1.00 66.0 no View details
trnfM-CAU-trnG-UCC LSC 90 0.0222 1.00 65.3 yes View details
matK LSC 1536 0.0039 1.00 60.9 yes View details
rps16 LSC 1087 0.0037 1.00 60.9 yes View details
trnT-UGU-trnL-UAA LSC 817 0.0037 1.00 60.9 yes View details
psaA-ycf3 LSC 624 0.0032 1.00 60.8 yes View details
ndhF-rpl32 SSC 888 0.0011 0.99 60.8 yes View details
ccsA SSC 978 0.0031 1.00 60.5 yes View details
petB LSC 1467 0.0027 1.00 60.4 yes View details
rpl32-trnL-UAG SSC 702 0.0028 1.00 60.4 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
trnK-UUU_p1 trnK-UUU TACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2759–2760 1.000 73.5
trnK-UUU_p2 trnK-UUU ACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2758–2759 1.000 73.5
trnK-UUU_p3 trnK-UUU ATACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2760–2761 1.000 69.5
trnK-UUU_p4 trnK-UUU TACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2759–2760 1.000 66.9
trnK-UUU_p5 trnK-UUU CAATGTCAACCAAGCCAGC CGTGCGGTGTAATTCCATTG 2756–2757 1.000 66.8
matK_p1 matK AGGGAACATTTCAGAAGAACA ATGCAACACCCTGTTTTGAC 1725 1.000 41.4
matK_p2 matK AGGGAACATTTCAGAAGAACA AATGCAACACCCTGTTTTGAC 1726 1.000 40.3
matK_p3 matK AGGGAACATTTCAGAAGAACA GCAACACCCTGTTTTGACCA 1723 1.000 40.3
matK_p4 matK AGGGAACATTTCAGAAGAACA TGCAACACCCTGTTTTGACC 1724 1.000 40.3
matK_p5 matK AGGGAACATTTCAGAAGAACAT ATGCAACACCCTGTTTTGAC 1725 1.000 40.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAAGAACT 690 1.000 66.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA GGTGCTCAACCTACAAGAACT 691 1.000 65.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACT 688 1.000 65.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACT 687 1.000 65.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCACTTAAAAGCCGAGT GGTGCTCAACCTACAAGAACT 689 1.000 64.5
rps16_p1 rps16 TGGCACGACATAAATCCAGT TCCCTATACCACTTTGCAATGA 1248 1.000 51.2
rps16_p2 rps16 TGGCACGACATAAATCCAGT TCAATTCCCTATACCACTTTGCA 1253 1.000 48.5
rps16_p3 rps16 TGGCACGACATAAATCCAGT TCCCTATACCACTTTGCAATGAA 1248 1.000 48.5
rps16_p4 rps16 TGGCACGACATAAATCCAGT TTCCCTATACCACTTTGCAATGA 1249 1.000 48.5
rps16_p5 rps16 TGGCACGACATAAATCCAGT CCCTATACCACTTTGCAATGA 1247 1.000 47.1
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACTCTACCAAGGGCTATAGTCA 1044 1.000 59.7
trnS-GCU-psbD_p2 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACTCTACCAAGGGCTATAGTCA 1030 1.000 56.7
trnS-GCU-psbD_p3 trnS-GCU-psbD AGTCCACTCAGCCATCTCTC ACTCTACCAAGGGCTATAGTCA 1025 1.000 55.9
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACTCTACCAAGGGCTATAGTCAT 1044 1.000 55.4
trnS-GCU-psbD_p5 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA AACTCTACCAAGGGCTATAGTCA 1045 1.000 55.0
trnfM-CAU-trnG-UCC_p1 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG AGCCTTCCAAGCTAACGATG 181 1.000 78.8
trnfM-CAU-trnG-UCC_p2 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCTAGCCTTCCAAGCTAACG 184 1.000 78.6
trnfM-CAU-trnG-UCC_p3 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG AGCCTTCCAAGCTAACGATG 166 1.000 78.4
trnfM-CAU-trnG-UCC_p4 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG CCTAGCCTTCCAAGCTAACG 169 1.000 78.2
trnfM-CAU-trnG-UCC_p5 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCAACGTCGACTATAACCCC 202 1.000 77.2

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
Himalayacalamus collaris NC_043941.1 139515 View on NCBI ↗
Himalayacalamus gyirongensis NC_043943.1 139592 View on NCBI ↗