Markers + reference

Aiphanes

2 species · Arecaceae · Arecales

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Species 2
Genome length 155–156 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 0.0009 1.00 48.2 yes View details
trnK-UUU-rps16 LSC 728 0.0097 1.00 64.7 yes View details
trnE-UUC-trnT-GGU LSC 284 0.0246 1.00 57.3 yes View details
accD-psaI LSC 584 0.0155 1.00 67.6 yes View details
rps8 LSC 399 0.0100 1.00 52.2 yes View details
ndhF-rpl32 SSC 297 0.0204 0.99 50.5 yes View details
ndhD SSC 1503 0.0047 1.00 49.7 yes View details
psaC-ndhE SSC 580 0.0232 0.97 74.7 yes View details
rps15-ycf1 SSC 383 0.0157 1.00 48.8 yes View details
ycf1 SSC 5505 0.0075 1.00 46.5 yes View details
rps19-psbA LSC 259 0.1957 0.53 81.7 no View details
rpl22-rps19 IRb 132 0.0379 1.00 72.2 yes View details
rpoA-rps11 LSC 79 0.0253 1.00 67.1 yes View details
trnH-GUG-rpl2 IRb 46 0.0217 1.00 65.0 yes View details
rpl2-trnH-GUG IRa 46 0.0217 1.00 65.0 yes View details
ycf3-trnS-GGA LSC 620 0.0065 1.00 62.5 yes View details
ndhJ-ndhK LSC 90 0.0222 1.00 62.5 yes View details
atpH-atpI LSC 823 0.0061 1.00 62.4 yes View details
rps16-trnQ-UUG LSC 1119 0.0054 1.00 62.1 yes View details
trnT-GGU-psbD LSC 981 0.0072 1.00 62.1 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 TTGCTCCATTCCTTCAACGA GTGCTTGGGAGTCCTTGAAA 1149 1.000 75.4
psbA_p2 psbA TTGCTCCATTCCTTCAACGA AATACGTGTGCTTGGGAGTC 1156 1.000 74.8
psbA_p3 psbA TGCTCCATTCCTTCAACGAT GTGCTTGGGAGTCCTTGAAA 1148 1.000 73.6
psbA_p4 psbA TGCTCCATTCCTTCAACGAT AATACGTGTGCTTGGGAGTC 1155 1.000 73.0
psbA_p5 psbA TGCTCCATTCCTTCAACGATT GTGCTTGGGAGTCCTTGAAA 1148 1.000 71.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GCTCAACCTACGGGAACTG 897–899 1.000 71.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GCTCAACCTACGGGAACTG 896–898 1.000 71.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GTGCTCAACCTACGGGAAC 899–901 1.000 70.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GTGCTCAACCTACGGGAAC 898–900 1.000 70.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACGGGAACTG 840–842 1.000 70.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1208–1210 1.000 79.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1206–1208 1.000 79.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1214–1216 1.000 79.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1215–1217 1.000 79.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1190–1192 1.000 78.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACGTTAGCCGC 912–947 1.000 75.5
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 884–919 1.000 75.5
atpH-atpI_p3 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACGTTAGCCGC 995–1030 1.000 75.4
atpH-atpI_p4 atpH-atpI TACCTTCTACAGCTTGGCCT TAGGTGAATCCATGGAGGGT 967–1002 1.000 75.4
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACGTTAGCCGC 968–1003 1.000 74.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 387 1.000 79.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 366 1.000 79.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TACCGCTGAGTTAAAAGGGC 352 1.000 78.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA TACCGCTGAGTTAAAAGGGC 331 1.000 78.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCGATGACTTACGCCTTACC 384 1.000 78.1
trnT-GGU-psbD_p1 trnT-GGU-psbD AACGGGCCCTTTTAACTCAG ACAAAAACGAAACGGTCCCT 1148–1150 1.000 77.9
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1143–1145 1.000 77.8
trnT-GGU-psbD_p3 trnT-GGU-psbD AACGGGCCCTTTTAACTCAG CCCTCCGTAACCAATCATCC 1132–1134 1.000 77.8
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA CCCTCCGTAACCAATCATCC 1127–1129 1.000 77.8
trnT-GGU-psbD_p5 trnT-GGU-psbD AACGGGCCCTTTTAACTCAG GCCAGACCAGCCTACAAAAA 1161–1163 1.000 76.8

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
Aiphanes chiribogensis NC_079765.1 155486 View on NCBI ↗
Aiphanes horrida NC_079766.1 155707 View on NCBI ↗