Markers + reference

Hemiboea

16 species · Gesneriaceae · Lamiales

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Species 16
Genome length 153–154 kb
Candidate markers 273
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1059 0.0025 1.00 36.5 yes View details
rps16 LSC 1124 0.0100 0.99 54.7 yes View details
trnS-GCU-trnG-UCC LSC 772 0.0215 0.98 65.9 yes View details
psaA-ycf3 LSC 726 0.0144 0.98 58.5 yes View details
petD LSC 1239 0.0075 1.00 54.3 yes View details
ycf1 IRb 807 0.0035 1.00 35.9 no View details
ndhF-rpl32 SSC 723 0.0143 1.00 63.9 yes View details
ycf1 SSC 5475 0.0122 0.99 52.7 yes View details
trnH-GUG-psbA LSC 200 0.0442 0.95 84.3 yes View details
rps2-rpoC2 LSC 200 0.0279 0.99 75.3 yes View details
trnK-UUU-rps16 LSC 805 0.0124 0.99 70.6 yes View details
trnE-UUC-trnT-GGU LSC 684 0.0080 0.99 70.5 yes View details
psbT-psbN LSC 65 0.0464 1.00 69.2 yes View details
ccsA-ndhD SSC 239 0.0214 1.00 69.0 yes View details
rps16-trnQ-UUG LSC 1064 0.0129 1.00 68.4 yes View details
trnT-GGU-psbD LSC 1322 0.0086 1.00 66.6 yes View details
ndhD-psaC SSC 101 0.0433 1.00 66.2 yes View details
rpl20-rps12 LSC 763 0.0073 1.00 62.5 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 85 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 CCGTGCTAACCTTGGTATGG 305–325 1.000 88.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 319–339 1.000 88.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 318–338 1.000 88.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 320–340 1.000 88.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 306–326 1.000 87.8
psbA_p1 psbA GATCCACTTGGCTACATCCG GAAAGCCGTGTGCAATGAAA 1634–1655 1.000 82.5
psbA_p2 psbA CAATCCACTGCCTTGATCCA GAAAGCCGTGTGCAATGAAA 1648–1669 1.000 82.5
psbA_p3 psbA AATCCACTGCCTTGATCCAC GAAAGCCGTGTGCAATGAAA 1647–1668 1.000 82.5
psbA_p4 psbA ACAATCCACTGCCTTGATCC GAAAGCCGTGTGCAATGAAA 1649–1670 1.000 82.4
psbA_p5 psbA CATCCGCCCCTCTACTATGA GAAAGCCGTGTGCAATGAAA 1620–1636 0.875 77.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 GTCGGGGTCTTCCAAACTTT TCTTGAAAGGGGTGCTCAAC 986–1023 1.000 87.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCTTGAAAGGGGTGCTCAAC 904–941 1.000 86.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCTTGAAAGGGGTGCTCAAC 903–940 1.000 86.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCGGGGTCTTCCAAACTTT GGTGCTCAACCTACAGGAAC 976–1013 1.000 85.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC TCTTGAAAGGGGTGCTCAAC 918–955 1.000 85.6
rps16_p1 rps16 GATACGAACCGAGCAGGAAG AAACATGCTGCTTATTGGCG 1720 0.062 39.0
rps16_p2 rps16 TAGATACGAACCGAGCAGGA AAACATGCTGCTTATTGGCG 1722 0.062 37.5
rps16_p3 rps16 GATACGAACCGAGCAGGAAG AACATGCTGCTTATTGGCGA 1719 0.062 36.9
rps16_p4 rps16 GATACGAACCGAGCAGGAAG ACATGCTGCTTATTGGCGAA 1718 0.062 36.9
rps16_p5 rps16 AGATACGAACCGAGCAGGAA AAACATGCTGCTTATTGGCG 1721 0.062 36.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TCGGAGGTTCGAATCCTTTC 1136–1160 1.000 81.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TAAGGCAACGGGTTTTGGTC 1163–1187 1.000 81.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TCGGAGGTTCGAATCCTTTC 1119–1143 1.000 81.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1146–1170 1.000 81.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA TCGGAGGTTCGAATCCTTTC 1137–1161 1.000 80.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 833–855 1.000 61.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 832–854 1.000 61.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 835–857 1.000 60.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 834–856 1.000 60.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 887–909 1.000 59.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (16)

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

Species Accession Length (bp) Link
Hemiboea fangii NC_079575.1 153695 View on NCBI ↗
Hemiboea integra NC_079574.1 153572 View on NCBI ↗
Hemiboea liana PX505290.1 153203 View on NCBI ↗
Hemiboea lutea PX505291.1 153547 View on NCBI ↗
Hemiboea malipoensis NC_080279.1 153331 View on NCBI ↗
Hemiboea parvibracteata NC_080280.1 153635 View on NCBI ↗
Hemiboea pterocaulis NC_082106.1 153159 View on NCBI ↗
Hemiboea purpurea NC_080277.1 152742 View on NCBI ↗
Hemiboea purpureotincta NC_080281.1 153642 View on NCBI ↗
Hemiboea roseoalba PX505292.1 153198 View on NCBI ↗
Hemiboea shimentaiensis PX505293.1 153577 View on NCBI ↗
Hemiboea sinovietnamica NC_079572.1 153186 View on NCBI ↗
Hemiboea subacaulis NC_080278.1 153211 View on NCBI ↗
Hemiboea subcapitata PX505294.1 153198 View on NCBI ↗
Hemiboea suiyangensis NC_080282.1 153190 View on NCBI ↗
Hemiboea yongfuensis NC_079573.1 153178 View on NCBI ↗