Markers + reference

Hessea

3 species · Amaryllidaceae · Asparagales

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Species 3
Genome length 158–158 kb
Candidate markers 271
Primer pairs 100

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 8 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU LSC 238 0.0252 1.00 54.0 yes View details
rps16-trnQ-UUG LSC 1475 0.0129 1.00 63.2 yes View details
psbK-psbI LSC 165 0.0242 1.00 62.3 yes View details
trnS-GCU-trnG-GCC LSC 1133 0.0124 0.99 58.9 yes View details
ycf4-cemA LSC 815 0.0123 1.00 57.5 yes View details
petA-psbJ LSC 1119 0.0176 0.98 68.2 yes View details
ndhF SSC 2220 0.0108 1.00 49.4 yes View details
rpl32-trnL-UAG SSC 714 0.0280 1.00 64.0 yes View details
ccsA SSC 966 0.0069 1.00 49.0 yes View details
ccsA-ndhD SSC 239 0.0335 1.00 61.9 yes View details
rps15-ycf1 SSC 374 0.0250 1.00 57.9 yes View details
trnR-UCU-atpA LSC 118 0.0282 1.00 70.5 yes View details
psbH-petB LSC 116 0.0187 0.92 65.6 yes View details
rps3-rpl22 LSC 33 0.0404 1.00 64.8 yes View details
trnF-GAA-ndhJ LSC 694 0.0068 0.99 63.7 yes View details
trnT-UGU-trnL-UAA LSC 650 0.0092 1.00 62.8 yes View details
psbC-trnS-UGA LSC 119 0.0504 1.00 62.1 yes View details
trnR-ACG-trnN-GUU IRb 604 0.0044 1.00 61.6 yes View details
trnN-GUU-trnR-ACG IRa 604 0.0044 1.00 61.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU CCCAGAAACAGGTTCACGAA TTGCGAAGATTAGGTTCGGG 915–921 1.000 80.9
psbA-trnK-UUU_p2 psbA-trnK-UUU CCCAGAAACAGGTTCACGAA CCATGTGGTGGTTGAATCCA 650–656 1.000 80.9
psbA-trnK-UUU_p3 psbA-trnK-UUU TAGCGGACTCGTTTTCAGTG TTGCGAAGATTAGGTTCGGG 1408–1414 1.000 80.3
psbA-trnK-UUU_p4 psbA-trnK-UUU ATGCAACAGCAATCCAAGGA TTGCGAAGATTAGGTTCGGG 1147–1153 1.000 80.3
psbA-trnK-UUU_p5 psbA-trnK-UUU GGTTACCAAGGAACCATGCA TTGCGAAGATTAGGTTCGGG 1368–1374 1.000 80.1
trnK-UUU_p1 trnK-UUU TGTCAACCAATCTCAACCGA AAAGGGGCGGTCTGTAAATG 2994–2999 1.000 72.6
trnK-UUU_p2 trnK-UUU TGTCAACCAATCTCAACCGA GGGCGGTCTGTAAATGTGAA 2990–2995 1.000 72.5
trnK-UUU_p3 trnK-UUU TGTCAACCAATCTCAACCGA TTCGATCCGCTCATTTTGCT 2934–2939 1.000 71.9
trnK-UUU_p4 trnK-UUU TGTCAACCAATCTCAACCGA GAAAAAGGGGCGGTCTGTAA 2997–2998 0.667 59.6
trnK-UUU_p5 trnK-UUU TGTCAACCAATCTCAACCGA AAAAAGGGGCGGTCTGTAAA 2996–2997 0.667 57.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCGAATCATGTCC GAGGTTCGAATCCTTCCGTC 1571–1573 1.000 80.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1548–1550 1.000 80.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCCACAGCGAATCATGTCC CTCGGAGGTTCGAATCCTTC 1575–1577 1.000 79.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1559–1561 1.000 79.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCGAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1569–1571 1.000 79.1
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ATTCCTCACGTCCGGGATTA 304 1.000 79.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TATTCCTCACGTCCGGGATT 305 1.000 79.4
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTATTCCTCACGTCCGGGAT 306 1.000 79.4
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGCCCGGATCGTTAGATAAG 283 1.000 78.3
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTATTCCTCACGTCCGGG 308 1.000 78.0
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGTCGCTTTAGTCCA CGGACGAATCACACTTTTACC 1198–1221 1.000 68.1
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGTCGCTTTAGTCCAC CGGACGAATCACACTTTTACC 1197–1220 1.000 68.1
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CGGAGAGAGAGGGATTCGAA CGGACGAATCACACTTTTACC 1251–1274 1.000 65.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGCAATCCGTCGCTTTAGTC CGGACGAATCACACTTTTACC 1200–1223 1.000 65.3
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CGTCGCTTTAGTCCACTCAG CGGACGAATCACACTTTTACC 1193–1216 1.000 65.1
trnR-UCU-atpA_p1 trnR-UCU-atpA AAAGAAAGGGGGAGAATGCG TTCGACCAAGACATTCACCG 327 1.000 78.3
trnR-UCU-atpA_p2 trnR-UCU-atpA AAAGGGGGAGAATGCGAAAG TTCGACCAAGACATTCACCG 323 1.000 78.3
trnR-UCU-atpA_p3 trnR-UCU-atpA GAAAGGGGGAGAATGCGAAA TTCGACCAAGACATTCACCG 324 1.000 78.2
trnR-UCU-atpA_p4 trnR-UCU-atpA GGGGAGAATGCGAAAGAAGA TTCGACCAAGACATTCACCG 319 1.000 76.4
trnR-UCU-atpA_p5 trnR-UCU-atpA AAAGGGGGAGAATGCGAAAG CCAAGACATTCACCGAGCAA 318 1.000 76.2

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
Hessea breviflora PP853210.1 157842 View on NCBI ↗
Hessea mathewsii PP853211.1 158032 View on NCBI ↗
Hessea pulcherrima PP853212.1 158053 View on NCBI ↗