Markers + reference

Paraboea

7 species · Gesneriaceae · Lamiales

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Species 7
Genome length 153–154 kb
Candidate markers 267
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 271 0.0926 0.86 74.3 yes View details
trnK-UUU-rps16 LSC 816 0.0329 0.99 76.0 yes View details
rps16-trnQ-UUG LSC 1068 0.0258 0.95 68.6 yes View details
trnS-GCU-trnR-UCU LSC 1798 0.0288 0.98 72.9 yes View details
atpF-atpH LSC 405 0.0390 0.97 74.8 yes View details
ycf3-trnS-GGA LSC 884 0.0261 0.98 69.4 yes View details
trnF-GAA-ndhJ LSC 688 0.0312 0.99 69.9 yes View details
ycf4-cemA LSC 825 0.0257 0.98 68.7 yes View details
petA-psbJ LSC 1029 0.0271 0.98 70.2 yes View details
ycf1 SSC 5469 0.0214 1.00 58.0 yes View details
ycf1-rps15 SSC 362 0.0419 1.00 74.9 yes View details
trnL-UAG-rpl32 SSC 862 0.0369 1.00 76.2 yes View details
ycf1 IRa 846 0.0057 1.00 52.2 no View details
psbI-trnS-GCU LSC 121 0.0415 1.00 77.0 yes View details
trnM-CAU-atpE LSC 203 0.0629 1.00 76.1 yes View details
rpl2-trnH-GUG IRa 50 0.0945 0.96 75.9 no View details
psaC-ndhD SSC 101 0.0682 0.95 73.2 yes View details
trnC-GCA-petN LSC 759 0.0207 0.98 72.5 yes View details
rps15-ndhH SSC 97 0.0481 1.00 71.9 yes View details
atpH-atpI LSC 1044 0.0221 0.99 71.3 yes View details
petN-psbM LSC 899 0.0190 0.99 71.3 yes View details
psaJ-rpl33 LSC 449 0.0320 1.00 71.1 yes View details
psaI-ycf4 LSC 428 0.0296 1.00 70.6 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 105 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 TCAGTGCTATGCATGGTTCC 666–720 1.000 89.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 665–719 1.000 89.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 680–734 1.000 88.8
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAGTGCTATGCATGGTTCC 679–733 1.000 88.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAGTGCTATGCATGGTTCC 681–735 1.000 88.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATACTTCCTTGAAAGGGGCG 939–949 1.000 83.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATACTTCCTTGAAAGGGGCG 938–948 1.000 83.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC ATACTTCCTTGAAAGGGGCG 953–963 1.000 82.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA ATACTTCCTTGAAAGGGGCG 948–958 1.000 82.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC ATACTTCCTTGAAAGGGGCG 925–935 1.000 80.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGATGTCGAGACAAGAGC GAGGTTCGAATCCTTCCGTC 1212–1238 1.000 88.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGATGTCGAGACAAGAGC AGCAGCTTGCCAAACAAAAG 1772–1798 1.000 88.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGATGTCGAGACAAGAGC CTTACAGCAGCTTGCCAAAC 1777–1803 1.000 88.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AACGATGTCGAGACAAGAGC GTGCGAATCGAGGGTTCATA 1920–2018 1.000 87.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AACGATGTCGAGACAAGAGC TGCGAATCGAGGGTTCATAC 1919–2017 1.000 87.1
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA CGAGTTATTCGTACCGAGGG 157–190 1.000 78.6
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA CGAGTTATTCGTACCGAGGG 157–190 1.000 76.3
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTATTCGTACCGAGGGTTCG 153–186 1.000 75.1
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTCGAATCCCTCTCTTTCCG 137–170 1.000 74.8
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GGGTTCGAATCCCTCTCTTT 140–173 1.000 73.7
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 1720–1935 1.000 72.9
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 1719–1934 1.000 72.9
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 1726–1941 1.000 72.2
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 1725–1940 1.000 72.2
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AGCAATCCGACGCTTTAGTC AGAAGACCTCTGTCCTATCCA 1722–1937 1.000 70.0
atpF-atpH_p1 atpF-atpH CCGTGCTGTGTCTAGACTTC TCCTTTCGTCTCGTTTCGAC 1325–1365 1.000 86.8
atpF-atpH_p2 atpF-atpH AAAAGGGTACAGCTGGTTGG GTCCTTTCGTCTCGTTTCGA 1140–1173 0.714 75.4
atpF-atpH_p3 atpF-atpH AAAAGGGTACAGCTGGTTGG TCCTTTCGTCTCGTTTCGAC 1139–1172 0.714 75.4
atpF-atpH_p4 atpF-atpH AAAAGGGTACAGCTGGTTGG AGTCCTTTCGTCTCGTTTCG 1141–1174 0.714 75.4
atpF-atpH_p5 atpF-atpH AAAAGGGTACAGCTGGTTGG CCTTTCGTCTCGTTTCGACT 1138–1171 0.714 75.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Paraboea clavisepala NC_058814.1 153398 View on NCBI ↗
Paraboea dictyoneura NC_058816.1 153406 View on NCBI ↗
Paraboea dolomitica NC_058810.1 153510 View on NCBI ↗
Paraboea glutinosa NC_058815.1 153505 View on NCBI ↗
Paraboea martinii NC_058818.1 153580 View on NCBI ↗
Paraboea rufescens NC_058817.1 153352 View on NCBI ↗
Paraboea wenshanensis NC_058809.1 154245 View on NCBI ↗