Markers + reference

Arnebia

5 species · Boraginaceae · Boraginales

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Species 5
Genome length 150–152 kb
Candidate markers 270
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 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 299 0.0955 1.00 81.8 yes View details
rps16-trnQ-UUG LSC 339 0.0200 1.00 51.6 yes View details
rpoB-trnC-GCA LSC 1230 0.0200 0.99 72.8 yes View details
accD-psaI LSC 388 0.1237 1.00 69.4 yes View details
ycf4-cemA LSC 963 0.0247 0.97 63.7 yes View details
petA-psbJ LSC 813 0.0270 0.99 73.5 yes View details
psbE-petL LSC 1167 0.0232 0.98 68.2 yes View details
petD LSC 1214 0.0211 1.00 55.3 yes View details
ycf1 IRb 1083 0.0018 1.00 39.6 no View details
rpl32-trnL-UAG SSC 557 0.0331 0.99 73.4 yes View details
ycf1 SSC 5364 0.0163 1.00 51.3 yes View details
trnG-UCC-trnR-UCU LSC 176 0.0375 1.00 80.9 yes View details
accD LSC 110 0.1627 1.00 76.0 yes View details
psaJ-rpl33 LSC 417 0.0296 1.00 72.1 yes View details
atpF-atpH LSC 387 0.0331 1.00 71.6 yes View details
atpA-atpF LSC 65 0.0385 1.00 70.6 yes View details
trnF-GAA-ndhJ LSC 641 0.0191 0.98 70.3 yes View details
trnS-GGA-rps4 LSC 296 0.0198 0.99 69.8 yes View details
trnK-UUU-rps16 LSC 680 0.0275 1.00 68.8 yes View details
trnM-CAU-atpE LSC 252 0.0344 0.98 68.6 yes View details
trnL-UAG-ccsA SSC 102 0.0353 1.00 68.3 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGACTTAGCTGCTGTCGAAG 252–366 1.000 85.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGACTTAGCTGCTGTCGAAG 266–380 1.000 85.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGACTTAGCTGCTGTCGAAG 265–379 1.000 85.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGACTTAGCTGCTGTCGAAG 267–381 1.000 85.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GGAATCACAATCCACTGCCT AGACTTAGCTGCTGTCGAAG 273–387 1.000 85.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAAAGGGTATGTTGCTGCCA 1494–1517 1.000 84.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGGTATGTTGCTGCCA 1493–1516 1.000 84.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TGAAGCCCTAGAGCCCTATC AAAAGGGTATGTTGCTGCCA 1639–1662 1.000 84.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCCCTTTCAGGATCAGTCGT AAAAGGGTATGTTGCTGCCA 1495–1518 1.000 84.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAAAGGGTATGTTGCTGCCA 1489–1512 1.000 83.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 408–438 1.000 83.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 410–440 1.000 82.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 401–431 1.000 82.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 411–441 1.000 82.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCGGATCATGTCTTT GAGGTTCGAATCCTTCCGTC 422–452 1.000 81.8
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAACAAATTGCGTCCAA 303–309 1.000 77.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAAACAAATTGCGTCCAA 306–312 1.000 76.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC TGGAAACAAATTGCGTCCAA 307–313 1.000 74.5
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT TGGAAACAAATTGCGTCCAA 292–298 1.000 74.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU TAACGATGCGGGTTCGATTC TGGAAACAAATTGCGTCCAA 291–297 1.000 74.1
atpA-atpF_p1 atpA-atpF ATGCCATCGCCTACTTGAAG TTGGGGGCGATGAAAGAAAT 209–212 1.000 80.5
atpA-atpF_p2 atpA-atpF CAATGCCATCGCCTACTTGA TTGGGGGCGATGAAAGAAAT 211–214 1.000 78.1
atpA-atpF_p3 atpA-atpF AATGCCATCGCCTACTTGAA TTGGGGGCGATGAAAGAAAT 210–213 1.000 77.5
atpA-atpF_p4 atpA-atpF ATGCCATCGCCTACTTGAAG GTTGGGGGCGATGAAAGAAA 210–213 1.000 76.3
atpA-atpF_p5 atpA-atpF GCCATCGCCTACTTGAAGTA TTGGGGGCGATGAAAGAAAT 207–210 1.000 76.1
atpF-atpH_p1 atpF-atpH TGGCCCAAAGAAACGAAAGA GGCTGGTTGTAGCATTAGCA 439–473 1.000 86.3
atpF-atpH_p2 atpF-atpH TGGCCCAAAGAAACGAAAGA TGGGCTGGTTGTAGCATTAG 441–475 1.000 85.0
atpF-atpH_p3 atpF-atpH TGGCCCAAAGAAACGAAAGA GCTGGTTGTAGCATTAGCAC 438–472 1.000 81.7
atpF-atpH_p4 atpF-atpH TGGCCCAAAGAAACGAAAGA TTTATGGGCTGGTTGTAGCA 445–479 1.000 81.2
atpF-atpH_p5 atpF-atpH TGGCCCAAAGAAACGAAAGA GGGCTGGTTGTAGCATTAGC 440–474 1.000 80.5

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
Arnebia decumbens NC_066703.1 149539 View on NCBI ↗
Arnebia fimbriata NC_066701.1 151927 View on NCBI ↗
Arnebia guttata NC_053780.1 150311 View on NCBI ↗
Arnebia szechenyi NC_066702.1 150867 View on NCBI ↗
Arnebia tibetana NC_053781.1 150465 View on NCBI ↗