Markers + reference

Aeginetia

2 species · Orobanchaceae · Lamiales

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Species 2
Genome length 55–86 kb
Candidate markers 123
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 123 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpA Genome 1344 0.1117 0.98 80.8 yes View details
atpF-atpH Genome 313 0.4623 0.64 69.7 yes View details
atpE Genome 381 0.3256 0.11 56.0 yes View details
rps16-trnQ-UUG Genome 1039 0.0918 0.91 85.5 yes View details
trnS-GGA-rps4 Genome 376 0.1559 0.90 81.9 yes View details
trnH-GUG-matK Genome 535 0.1298 0.92 81.7 yes View details
rrn16-rrn23 Genome 1402 0.0572 0.96 81.6 yes View details
rps11-rpl36 Genome 84 0.1772 0.94 79.1 yes View details
trnY-GUA-trnE-UUC Genome 63 0.1270 1.00 78.5 yes View details
atpB Genome 1400 0.0892 0.86 78.5 yes View details
rps12-clpP Genome 119 0.1524 0.88 78.4 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-matK_p1 trnH-GUG-matK TTGCCTTCATCCATTTGGCT TCTGGCTTCAAAAGGAACGT 1236–1388 1.000 85.9
trnH-GUG-matK_p2 trnH-GUG-matK TTGCCTTCATCCATTTGGCT TGGCTTCAAAAGGAACGTCT 1234–1386 1.000 85.9
trnH-GUG-matK_p3 trnH-GUG-matK TTGCCTTCATCCATTTGGCT TGGGGCATTGACTAAAGCAA 972 0.500 57.1
trnH-GUG-matK_p4 trnH-GUG-matK TTGCCTTCATCCATTTGGCT TTGGGGCATTGACTAAAGCA 973 0.500 57.1
trnH-GUG-matK_p5 trnH-GUG-matK TTGCCTTCATCCATTTGGCT AGCGAACCTTTGGTTGGTTA 1299 0.500 56.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CTCTTTTCCTTCTCGTCGGG CGTAGGTTCGAATCCTTCCG 1126–1208 1.000 88.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CTCTTTTCCTTCTCGTCGGG TGGCTAAGTGGTAAGGCAAC 1165–1247 1.000 88.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CTCTTTTCCTTCTCGTCGGG CTAAGTGGTAAGGCAACGGG 1162–1244 1.000 87.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGCTCTTTTCCTTCTCGTCG CGTAGGTTCGAATCCTTCCG 1128–1210 1.000 85.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCTTTTCCTTCTCGTCGGGA CGTAGGTTCGAATCCTTCCG 1125–1207 1.000 85.7
atpA_p1 atpA ACGGAAAGAGAGGGATTCGA AGTTGTTTTACCGCCGAGTT 1966 0.500 58.5
atpA_p2 atpA GTTGCCTTACCACTTAGCCA AGTTGTTTTACCGCCGAGTT 2158 0.500 58.1
atpA_p3 atpA TTGCCTTACCACTTAGCCAC AGTTGTTTTACCGCCGAGTT 2157 0.500 58.1
atpA_p4 atpA CCCGTTGCCTTACCACTTAG AGTTGTTTTACCGCCGAGTT 2161 0.500 57.5
atpA_p5 atpA AAAAGATATGCCCTGGGACG AGTTGTTTTACCGCCGAGTT 2215 0.500 56.9
atpF-atpH_p1 atpF-atpH AACTCGGCGGTAAAACAACT GAGACAACTCGAGGCTGAAG 824 0.500 59.6
atpF-atpH_p2 atpF-atpH AACTCGGCGGTAAAACAACT TGACCCTGACCTTGCAGATA 1217 0.500 59.3
atpF-atpH_p3 atpF-atpH AACTCGGCGGTAAAACAACT TGTAGGGCTTGCTTCTTTGG 887 0.500 58.9
atpF-atpH_p4 atpF-atpH AACTCGGCGGTAAAACAACT ATTTCTGCTGCTTCTGTGCT 922 0.500 58.9
atpF-atpH_p5 atpF-atpH AACTCGGCGGTAAAACAACT CAACTCGAGGCTGAAGGAAA 820 0.500 58.3
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC ACGAATTTACAGTCCGTCCC CAAGGAGACAGCGAGGATTC 141–156 1.000 80.8
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC CAGTCCGTCCCTATTAACCG CAAGGAGACAGCGAGGATTC 132–147 1.000 80.0
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC CTATTAACCGCTCGGGCATC CAAGGAGACAGCGAGGATTC 122–137 1.000 79.8
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC ACGAATTTACAGTCCGTCCC GAGGATTCGAATTCCCCTGG 129–144 1.000 79.6
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC GCCAACGAATTTACAGTCCG CAAGGAGACAGCGAGGATTC 145–160 1.000 79.5
trnS-GGA-rps4_p1 trnS-GGA-rps4 ATGTAGGAGAGATGGCCGAG AAATGAATTGCTAGTCGTAGA 493–510 1.000 52.0
trnS-GGA-rps4_p2 trnS-GGA-rps4 ATGTAGGAGAGATGGCCGAG AATGAATTGCTAGTCGTAGAA 492–509 1.000 52.0
trnS-GGA-rps4_p3 trnS-GGA-rps4 ATGTAGGAGAGATGGCCGAG TGCTAGTCGTAGAATATTATTCTCGT 485–502 1.000 52.0
trnS-GGA-rps4_p4 trnS-GGA-rps4 ATGTAGGAGAGATGGCCGAG AAATGAATTGCTAGTCGTAGAA 493–510 1.000 52.0
trnS-GGA-rps4_p5 trnS-GGA-rps4 ATGTAGGAGAGATGGCCGAG ATGAATTGCTAGTCGTAGAAT 491–508 1.000 52.0

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
Aeginetia indica NC_086657.1 55394 View on NCBI ↗
Aeginetia sinensis NC_086658.1 86073 View on NCBI ↗