Markers + reference

Pinanga

4 species · Arecaceae · Arecales

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Species 4
Genome length 157–158 kb
Candidate markers 260
Primer pairs 85

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0122 1.00 55.8 yes View details
trnS-GCU-trnS-CGA LSC 1360 0.0574 0.71 79.8 yes View details
psbC LSC 1422 0.0007 1.00 38.8 yes View details
petA-psbJ LSC 1019 0.0164 1.00 64.1 yes View details
rpl2 IRb 1483 0.0000 1.00 26.1 no View details
ndhF-trnL-UAG SSC 1324 0.0256 0.96 80.0 yes View details
psaC-ndhE SSC 451 0.0200 0.93 72.3 yes View details
ycf1 SSC 5430 0.0043 0.98 49.2 yes View details
rpl2 IRa 1483 0.0000 1.00 26.1 yes View details
rpl22-rps19 LSC 122 0.0273 0.98 75.1 yes View details
trnH-GUG-psbA LSC 270 0.1481 0.80 75.0 no View details
psbC-trnS-UGA LSC 137 0.0438 1.00 68.1 yes View details
trnT-GGU-psbD LSC 1063 0.0074 1.00 63.9 yes View details
atpF-atpH LSC 540 0.0038 0.98 61.6 yes View details
trnK-UUU-rps16 LSC 734 0.0043 1.00 61.3 yes View details
atpH-atpI LSC 822 0.0024 1.00 61.0 yes View details
ycf3-trnS-GGA LSC 617 0.0032 1.00 61.0 yes View details
trnF-GAA-ndhJ LSC 721 0.0058 1.00 60.7 yes View details
petD LSC 1254 0.0025 1.00 60.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TCAACGATTCATATACACTAAGACA GTGCTTGGGAGTCCTTGAAA 1136 1.000 42.5
psbA_p2 psbA CAACGATTCATATACACTAAGACA GTGCTTGGGAGTCCTTGAAA 1135 1.000 42.5
psbA_p3 psbA TCAACGATTCATATACACTAAGACAA GTGCTTGGGAGTCCTTGAAA 1136 1.000 42.5
psbA_p4 psbA TTCAACGATTCATATACACTAAGACA GTGCTTGGGAGTCCTTGAAA 1137 1.000 42.5
psbA_p5 psbA TCAACGATTCATATACACTAAGACA AATACGTGTGCTTGGGAGTC 1143 1.000 42.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GCTCAACCTACGGGAACTG 895–901 1.000 71.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GCTCAACCTACGGGAACTG 894–900 1.000 71.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GTGCTCAACCTACGGGAAC 897–903 1.000 70.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GTGCTCAACCTACGGGAAC 896–902 1.000 70.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACGGGAACTG 838–844 1.000 70.4
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1039–1505 1.000 62.8
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 1042–1508 1.000 61.7
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 1041–1507 1.000 61.7
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 1095–1561 1.000 60.9
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 1040–1506 1.000 60.8
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG ATTTATGGACTGGTCGTGGC 652–663 1.000 80.6
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAAGGAA ATTTATGGACTGGTCGTGGC 624–635 1.000 76.3
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCGTTAGCACTTTTGTTTGC 634–645 1.000 73.7
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAAGGAAA ATTTATGGACTGGTCGTGGC 624–635 1.000 73.2
atpF-atpH_p5 atpF-atpH GTGACCCAAGGAAAGGAAAGA ATTTATGGACTGGTCGTGGC 622–633 1.000 71.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACGTTAGCCGC 911–948 1.000 75.7
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 883–920 1.000 75.7
atpH-atpI_p3 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACGTTAGCCGC 994–1031 1.000 75.6
atpH-atpI_p4 atpH-atpI TACCTTCTACAGCTTGGCCT TAGGTGAATCCATGGAGGGT 966–1003 1.000 75.6
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACGTTAGCCGC 967–1004 1.000 75.1
trnT-GGU-psbD_p1 trnT-GGU-psbD AACGGGCCCTTTTAACTCAG ACAAAAACGAAACGGTCCCT 1232–1234 1.000 78.3
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1227–1229 1.000 78.2
trnT-GGU-psbD_p3 trnT-GGU-psbD AACGGGCCCTTTTAACTCAG CCCTCCGTAACCAATCATCC 1216–1218 1.000 78.2
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA CCCTCCGTAACCAATCATCC 1211–1213 1.000 78.2
trnT-GGU-psbD_p5 trnT-GGU-psbD AACGGGCCCTTTTAACTCAG GCCAGACCAGCCTACAAAAA 1245–1247 1.000 77.2

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
Pinanga arinasae NC_081962.1 156773 View on NCBI ↗
Pinanga baviensis NC_079804.1 157533 View on NCBI ↗
Pinanga coronata NC_067845.1 157724 View on NCBI ↗
Pinanga sylvestris NC_079805.1 157692 View on NCBI ↗