Markers + reference

Chamaedorea

5 species · Arecaceae · Arecales

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Species 5
Genome length 156–157 kb
Candidate markers 271
Primer pairs 95

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0126 1.00 48.6 yes View details
trnQ-UUG-psbK LSC 329 0.0164 1.00 45.5 yes View details
psbK-psbI LSC 396 0.0411 1.00 72.2 yes View details
trnS-GCU-trnG-UCC LSC 1283 0.0178 0.95 57.7 yes View details
atpH-atpI LSC 832 0.0161 0.99 61.5 yes View details
ndhC-trnV-UAC LSC 971 0.0183 0.99 66.8 yes View details
accD-psaI LSC 985 0.0240 0.88 58.4 yes View details
ycf4-cemA LSC 224 0.0286 1.00 50.1 yes View details
rpl16 LSC 1508 0.0132 0.99 60.6 yes View details
psaC-ndhE SSC 659 0.0270 0.94 78.4 yes View details
rps19-psbA LSC 150 0.1138 0.89 67.2 no View details
trnP-UGG-psaJ LSC 376 0.0172 1.00 63.9 yes View details
petN-psbM LSC 699 0.0115 0.99 62.0 yes View details
petA-psbJ LSC 1009 0.0146 1.00 60.9 yes View details
psbE-petL LSC 1286 0.0069 1.00 60.2 yes View details
psaJ-rpl33 LSC 547 0.0124 0.99 58.7 yes View details
trnT-GGU-psbD LSC 1029 0.0098 1.00 57.4 yes View details
ndhF-rpl32 SSC 295 0.0297 0.98 56.3 yes View details
rps3-rpl22 LSC 66 0.0384 1.00 56.1 yes View details
trnT-UGU-trnL-UAA LSC 801 0.0130 1.00 56.0 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TTGCTCCATTTCTTCAACGA TGGGAGTCCTTGAAAATTGA 1144–1149 1.000 42.2
psbA_p2 psbA TTGCTCCATTTCTTCAACGA TGGGAGTCCTTGAAAATTGAA 1144–1149 1.000 42.2
psbA_p3 psbA TTGCTCCATTTCTTCAACGA TTGGGAGTCCTTGAAAATTGA 1145–1150 1.000 42.2
psbA_p4 psbA TGCTCCATTTCTTCAACGAT TGGGAGTCCTTGAAAATTGA 1143–1148 1.000 42.2
psbA_p5 psbA GCTCCATTTCTTCAACGATTCA TGGGAGTCCTTGAAAATTGA 1142–1147 1.000 42.2
trnQ-UUG-psbK_p1 trnQ-UUG-psbK CCAAAACCCGCTGCCTTA AGACAGAATTAAGACAGATGCAGA 411–417 1.000 42.3
trnQ-UUG-psbK_p2 trnQ-UUG-psbK AAAACCCGCTGCCTTACC AGACAGAATTAAGACAGATGCAGA 409–415 1.000 42.3
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CAAAACCCGCTGCCTTACC AGACAGAATTAAGACAGATGCAGA 410–416 1.000 42.3
trnQ-UUG-psbK_p4 trnQ-UUG-psbK CCAAAACCCGCTGCCTTAC AGACAGAATTAAGACAGATGCAGA 411–417 1.000 42.3
trnQ-UUG-psbK_p5 trnQ-UUG-psbK CCAAAACCCGCTGCCTTA GACAGAATTAAGACAGATGCAGA 410–416 1.000 42.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGATTACGCCCTGGATCAT 519–524 1.000 83.3
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT AGGATTACGCCCTGGATCAT 516–521 1.000 81.3
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT AGGATTACGCCCTGGATCAT 517–522 1.000 81.3
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT AGGATTACGCCCTGGATCAT 518–523 1.000 81.2
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGCCCTGGATCATT 518–523 1.000 80.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCACCGCTTTAGTCCA ACGAATCACACTTTTACCACT 256–1412 1.000 57.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCACCGCTTTAGTCCAC ACGAATCACACTTTTACCACT 255–1411 1.000 57.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CTCGTACAGCGGATTAGCAA ACGAATCACACTTTTACCACT 273–1429 1.000 56.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AACTCGTACAGCGGATTAGC ACGAATCACACTTTTACCACT 275–1431 1.000 56.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCACCGCTTTAGTC ACGAATCACACTTTTACCACT 258–1414 1.000 56.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 884–941 1.000 80.5
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACGTTAGCCGC 912–969 1.000 80.4
atpH-atpI_p3 atpH-atpI TACCTTCTACAGCTTGGCCT TAGGTGAATCCATGGAGGGT 967–1024 1.000 80.0
atpH-atpI_p4 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACGTTAGCCGC 995–1052 1.000 79.9
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACGTTAGCCGC 968–1025 1.000 79.5
petN-psbM_p1 petN-psbM GTCTCACTTGGGCTGCTTTA TGCTACTGCACTGTTCATTCT 854–867 1.000 71.1
petN-psbM_p2 petN-psbM ACTTGGGCTGCTTTAATGGT TGCTACTGCACTGTTCATTCT 849–862 1.000 70.1
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 799–812 1.000 70.0
petN-psbM_p4 petN-psbM GTAAGTCTCACTTGGGCTGC TGCTACTGCACTGTTCATTCT 858–871 1.000 68.1
petN-psbM_p5 petN-psbM TAAGTCTCACTTGGGCTGCT TGCTACTGCACTGTTCATTCT 857–870 1.000 67.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Chamaedorea cataractarum NC_079719.1 156988 View on NCBI ↗
Chamaedorea costaricana NC_079720.1 157002 View on NCBI ↗
Chamaedorea elegans NC_051509.1 156922 View on NCBI ↗
Chamaedorea linearis NC_079774.1 155925 View on NCBI ↗
Chamaedorea seifrizii NC_079721.1 156897 View on NCBI ↗