Markers + reference

Melocalamus

3 species · Poaceae · Poales

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Species 3
Genome length 139–139 kb
Candidate markers 263
Primer pairs 90

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 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 557 0.0024 1.00 40.8 yes View details
trnS-GCU-psbD LSC 998 0.0027 1.00 60.6 yes View details
trnG-UCC-trnT-GGU LSC 2034 0.0010 1.00 58.3 yes View details
atpI-atpH LSC 820 0.0033 1.00 48.3 yes View details
trnT-UGU-trnL-UAA LSC 806 0.0017 1.00 47.3 yes View details
rbcL-psaI LSC 1246 0.0027 1.00 48.0 yes View details
ndhB IRb 2245 0.0000 1.00 31.4 no View details
ndhF SSC 2352 0.0014 1.00 57.9 yes View details
rpl32-trnL-UAG SSC 718 0.0046 1.00 48.8 yes View details
ndhB IRa 2245 0.0000 1.00 31.4 yes View details
ndhB-trnL-CAA LSC 565 0.0142 1.00 67.0 yes View details
ndhC-trnV-UAC LSC 925 0.0007 0.97 61.8 yes View details
trnC-GCA-rpoB LSC 1170 0.0006 1.00 60.9 yes View details
rps19-psbA LSC 137 0.0081 0.91 59.7 no View details
petB LSC 1476 0.0009 1.00 59.4 yes View details
atpF LSC 1402 0.0005 1.00 59.1 yes View details
rpoC2 LSC 4560 0.0003 1.00 53.4 yes View details
ndhF-rpl32 SSC 766 0.0009 1.00 51.5 yes View details
rpl16 LSC 1509 0.0009 1.00 49.5 yes View details
atpH-atpF LSC 456 0.0000 1.00 47.3 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAAGAACT 691 1.000 66.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA GGTGCTCAACCTACAAGAACT 692 1.000 65.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACT 689 1.000 65.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACT 688 1.000 65.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCACTTAAAAGCCGAGT GGTGCTCAACCTACAAGAACT 690 1.000 64.4
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1143–1145 1.000 78.7
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1130–1132 1.000 78.1
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1129–1131 1.000 75.7
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1122–1124 1.000 75.5
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1116–1118 1.000 75.1
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2169–2170 1.000 42.7
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTACGTCTTACCATGGCA 2182–2183 1.000 41.9
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTACCATGGC 2183–2184 1.000 41.9
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC CCATGGCATTACTCTACCACC 2172–2173 1.000 41.6
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2171–2172 1.000 41.6
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1237–1254 1.000 78.1
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1236–1253 1.000 78.1
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AAGTTCTTCTGCCAAGCCTT 1301–1318 1.000 77.6
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AGTTCTTCTGCCAAGCCTTG 1300–1317 1.000 77.5
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CAAGTTCTTCTGCCAAGCCT 1302–1319 1.000 77.5
rpoC2_p1 rpoC2 TCGAATCCTACTCAGCCGAA AAAACTCTGTTGTTCCGCGT 277 1.000 73.4
rpoC2_p2 rpoC2 CCTACTCAGCCGAAAAAGGG AAAACTCTGTTGTTCCGCGT 271 1.000 73.2
rpoC2_p3 rpoC2 CTACTCAGCCGAAAAAGGGG AAAACTCTGTTGTTCCGCGT 270 1.000 73.2
rpoC2_p4 rpoC2 TTCGAATCACTGACTCAGGC AAAACTCTGTTGTTCCGCGT 324 1.000 72.3
rpoC2_p5 rpoC2 GGCCCATTGTCGAATCCTAC AAAACTCTGTTGTTCCGCGT 307 1.000 72.0
atpI-atpH_p1 atpI-atpH TAGCCGCAGCCTATATAGGT GCAGTACCTTGACCAACTCC 956 1.000 74.6
atpI-atpH_p2 atpI-atpH TAGCCGCAGCCTATATAGGT AAGCAGCAGCAATTAGTGGA 889 1.000 74.5
atpI-atpH_p3 atpI-atpH TAGCCGCAGCCTATATAGGT GCCAATCCAGCAGCAATAAC 911 1.000 74.4
atpI-atpH_p4 atpI-atpH TAGCCGCAGCCTATATAGGT ATAACGGAAGCAGCAGCAAT 896 1.000 74.2
atpI-atpH_p5 atpI-atpH ATTTTTGCAACGTTAGCCGC GCAGTACCTTGACCAACTCC 969 1.000 74.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Melocalamus arrectus NC_050745.1 139474 View on NCBI ↗
Melocalamus compactiflorus var. fimbriatus PV976826.1 139440 View on NCBI ↗
Melocalamus scandens PV976834.1 139440 View on NCBI ↗