Markers + reference

Primulina

22 species · Gesneriaceae · Lamiales

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Species 22
Genome length 152–154 kb
Candidate markers 272
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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 332 0.0657 0.97 76.2 yes View details
rps16-trnQ-UUG LSC 1064 0.0203 0.98 68.5 yes View details
trnS-GCU-trnG-UCC LSC 757 0.0244 0.99 72.0 yes View details
atpF LSC 1254 0.0089 1.00 53.9 yes View details
psaA-ycf3 LSC 788 0.0315 0.96 82.0 yes View details
trnT-GGU-trnL-UAA LSC 655 0.0159 0.99 74.5 yes View details
ycf1 IRb 786 0.0054 1.00 46.4 no View details
ndhF-rpl32 SSC 746 0.0282 0.59 65.2 yes View details
rps15-ycf1 SSC 376 0.0236 1.00 63.3 yes View details
ycf1 SSC 5481 0.0165 0.99 62.7 yes View details
petB-petD LSC 928 0.0177 0.99 82.7 yes View details
rps4-trnT-GGU LSC 374 0.0297 0.97 79.7 yes View details
rpl32-trnL-UAG SSC 817 0.0193 0.99 76.9 yes View details
trnE-UUC-trnT-GGU LSC 579 0.0168 1.00 75.9 yes View details
trnT-GGU-psbD LSC 1301 0.0164 1.00 75.3 yes View details
atpF-atpH LSC 387 0.0171 0.97 74.4 yes View details
psbA-trnK-UUU LSC 238 0.0189 1.00 72.9 yes View details
trnS-GCU-rps4 LSC 303 0.0272 1.00 72.7 yes View details
petN-psbM LSC 991 0.0193 1.00 72.6 yes View details
clpP-psbB LSC 460 0.0182 1.00 70.3 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 95 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 TCGGTCAGGAGGAAGAAACT 647–773 1.000 90.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGGTCAGGAGGAAGAAACT 661–787 1.000 90.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCGGTCAGGAGGAAGAAACT 660–786 1.000 90.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCGGTCAGGAGGAAGAAACT 662–788 1.000 90.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GTTATACAACGGCGGTCCTT 1048–1174 1.000 90.4
psbA-trnK-UUU_p1 psbA-trnK-UUU TACAGAAGCGACCCCATAGG CTAGTTCCGGGTTCGAATCC 314–346 1.000 85.5
psbA-trnK-UUU_p2 psbA-trnK-UUU ATCCAGTTACAGAAGCGACC CTAGTTCCGGGTTCGAATCC 321–353 0.955 82.0
psbA-trnK-UUU_p3 psbA-trnK-UUU AGTTACAGAAGCGACCCCAT CTAGTTCCGGGTTCGAATCC 317–349 0.955 81.7
psbA-trnK-UUU_p4 psbA-trnK-UUU AGACGGTTTTCAGTGTTGGT CTAGTTCCGGGTTCGAATCC 352 0.045 36.7
psbA-trnK-UUU_p5 psbA-trnK-UUU AGACGGTTTTCAGTGTTGGT ATGAAAAATGCAAGCACGGC 432 0.045 34.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGATGTCGAGACAAGAGC AGCAGCTTGCCAAACAAAAG 1285–1855 1.000 90.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGATGTCGAGACAAGAGC CTTACAGCAGCTTGCCAAAC 1290–1860 1.000 90.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG AGCAGCTTGCCAAACAAAAG 1214–1784 0.955 88.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG CTTACAGCAGCTTGCCAAAC 1219–1789 0.955 88.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AACGATGTCGAGACAAGAGC GAGGTTCGAATCCTTCCGTC 1042–1247 0.409 61.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 709–865 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 708–864 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 712–868 1.000 62.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 711–867 1.000 62.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 710–866 1.000 62.6
atpF_p1 atpF CAATACCATCGCCCACTTGA TTTCCGTGGACTTGTCGTTT 1745–1895 1.000 90.1
atpF_p2 atpF CACCCGCCATTACTTCATCA TTTCCGTGGACTTGTCGTTT 1781–1931 1.000 89.9
atpF_p3 atpF CACTTGAAGTACGGTACCGG TTTCCGTGGACTTGTCGTTT 1732–1882 0.955 88.3
atpF_p4 atpF CCACTTGAAGTACGGTACCG TTTCCGTGGACTTGTCGTTT 1733–1883 0.955 88.3
atpF_p5 atpF CACTTGAAGTACGGTACCGG TAGGGCTTGCTTCTATCGGA 1967–2117 0.955 87.5
atpF-atpH_p1 atpF-atpH CCAGTGGCCTAAAGAAACGA AGGCAGAGGGAAAGATACGA 493–545 1.000 87.3
atpF-atpH_p2 atpF-atpH TTAAATCCGAAACTCCCGGC AGGCAGAGGGAAAGATACGA 519–571 1.000 86.4
atpF-atpH_p3 atpF-atpH CCAGTGGCCTAAAGAAACGA GCAGAGGGAAAGATACGAGG 491–543 1.000 84.5
atpF-atpH_p4 atpF-atpH CCAGTGGCCTAAAGAAACGA GGCAGAGGGAAAGATACGAG 492–544 1.000 84.5
atpF-atpH_p5 atpF-atpH CCAGTGGCCTAAAGAAACGA GAGGCAGAGGGAAAGATACG 494–546 1.000 84.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (22)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Primulina brachytricha var. magnibracteata MF177037.1 153723 View on NCBI ↗
Primulina cardaminifolia NC_068075.1 153300 View on NCBI ↗
Primulina cordata NC_065792.1 153786 View on NCBI ↗
Primulina eburnea NC_036100.1 152963 View on NCBI ↗
Primulina fimbrisepala NC_065793.1 153089 View on NCBI ↗
Primulina flexusa PP954907.1 152933 View on NCBI ↗
Primulina fordii PP954903.1 153315 View on NCBI ↗
Primulina hedyotidea NC_069200.1 153297 View on NCBI ↗
Primulina hezhouensis NC_065794.1 153556 View on NCBI ↗
Primulina liboensis NC_036101.1 152989 View on NCBI ↗
Primulina lutea NC_065795.1 153262 View on NCBI ↗
Primulina malingheensis PP954906.1 153106 View on NCBI ↗
Primulina medica NC_065796.1 153523 View on NCBI ↗
Primulina obtusidentata PP954904.1 152869 View on NCBI ↗
Primulina ophiopogoides NC_054175.1 152718 View on NCBI ↗
Primulina pengii NC_065797.1 152359 View on NCBI ↗
Primulina sclerophylla NC_065798.1 153185 View on NCBI ↗
Primulina secundiflora PP954908.1 153099 View on NCBI ↗
Primulina silaniae PP954909.1 153364 View on NCBI ↗
Primulina tenuituba PP954910.1 153214 View on NCBI ↗
Primulina vestita PP954911.1 153184 View on NCBI ↗
Primulina xingyiensis PX316975.1 153114 View on NCBI ↗