Markers + reference

Erythranthe

17 species · Phrymaceae · Lamiales

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Species 17
Genome length 153–154 kb
Candidate markers 269
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 410 0.0483 1.00 74.0 yes View details
trnK-UUU-rps16 LSC 906 0.0287 1.00 69.8 yes View details
rps16-trnQ-UUG LSC 1153 0.0333 1.00 69.7 yes View details
trnS-GCU-trnG-UCC LSC 684 0.0271 1.00 62.3 yes View details
atpH-atpI LSC 1024 0.0206 1.00 59.3 yes View details
ndhC-trnV-UAC LSC 1189 0.0234 1.00 63.9 yes View details
ndhF SSC 2244 0.0154 1.00 46.2 yes View details
rpl32-trnL-UAG SSC 450 0.0383 0.99 68.0 yes View details
ycf1 SSC 5586 0.0214 1.00 63.5 yes View details
trnC-GCA-petN LSC 846 0.0235 1.00 68.7 yes View details
trnG-GCC-trnfM-CAU LSC 172 0.0443 1.00 63.8 yes View details
rps15-ycf1 SSC 319 0.0363 0.98 62.5 yes View details
trnW-CCA-trnP-UGG LSC 172 0.0370 1.00 62.2 yes View details
psbI-trnS-GCU LSC 121 0.0574 1.00 61.9 yes View details
petN-psbM LSC 1005 0.0223 1.00 61.9 yes View details
ndhF-rpl32 SSC 531 0.0292 1.00 61.6 yes View details
ycf3-trnS-GGA LSC 662 0.0244 1.00 60.1 yes View details
psaA-ycf3 LSC 805 0.0247 1.00 60.0 yes View details
rpoB-trnC-GCA LSC 1205 0.0222 1.00 59.2 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 TTCCCTCTAGACCTAGCTGC 467–607 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 481–621 1.000 90.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 480–620 1.000 90.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 482–622 1.000 90.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC TTCCCTCTAGACCTAGCTGC 472–612 1.000 86.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAGCGGAAGTTTTTAAGGAACT 956–1008 1.000 59.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAGCGGAAGTTTTTAAGGAACT 955–1007 1.000 59.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGCGGAAGTTTTTAAGGAAC 954–1006 1.000 59.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGCGGAAGTTTTTAAGGAAC 953–1005 1.000 59.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AAAGCGGAAGTTTTTAAGGAACT 970–1022 1.000 58.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1172–1304 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1186–1318 1.000 88.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1176–1308 1.000 85.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1202–1334 1.000 85.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1164–1296 1.000 85.1
psbI-trnS-GCU_p1 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG TGGACTAAAGCGTCGGATTG 718–730 1.000 87.6
psbI-trnS-GCU_p2 psbI-trnS-GCU CTTTTGTTTGGCAAGCTGCT TGGACTAAAGCGTCGGATTG 723–735 1.000 87.5
psbI-trnS-GCU_p3 psbI-trnS-GCU CTTTTGTTTGGCAAGCTGCT GTGGACTAAAGCGTCGGATT 724–736 1.000 87.5
psbI-trnS-GCU_p4 psbI-trnS-GCU TTCTTGGCTTGGATAGTCGC TGGACTAAAGCGTCGGATTG 586–588 0.706 68.6
psbI-trnS-GCU_p5 psbI-trnS-GCU TTCTTGGCTTGGATAGTCGC GTGGACTAAAGCGTCGGATT 587–589 0.706 68.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 736–764 1.000 58.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC ACGAATCACACTTTTACCACT 731–759 1.000 57.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AACGAATCACACTTTTACCACT 737–765 1.000 56.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC AACGAATCACACTTTTACCACT 732–760 1.000 55.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TAGTCCACTCAGCCATCTCT ACGAATCACACTTTTACCACT 732–760 1.000 54.8
atpH-atpI_p1 atpH-atpI CAACTCCAGGCCCAATAGAC GGCAAATAGGGGGTTTCCAA 1716–1774 1.000 88.0
atpH-atpI_p2 atpH-atpI CAACTCCAGGCCCAATAGAC TTGGCAAATAGGGGGTTTCC 1718–1776 1.000 88.0
atpH-atpI_p3 atpH-atpI CAAATCACCCCTTCCCGTAG GGCAAATAGGGGGTTTCCAA 2029–2079 0.941 85.4
atpH-atpI_p4 atpH-atpI CAAATCACCCCTTCCCGTAG TTGGCAAATAGGGGGTTTCC 2031–2081 0.941 85.4
atpH-atpI_p5 atpH-atpI CAAATCACCCCTTCCCGTAG TTCGGAACCCACAAACCATT 1939–1989 0.941 85.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Erythranthe arvensis NC_068029.1 153192 View on NCBI ↗
Erythranthe caespitosa NC_068030.1 153153 View on NCBI ↗
Erythranthe cardinalis NC_068031.1 153680 View on NCBI ↗
Erythranthe decora NC_068032.1 153192 View on NCBI ↗
Erythranthe glaucescens NC_068034.1 153131 View on NCBI ↗
Erythranthe guttata NC_068035.1 153168 View on NCBI ↗
Erythranthe laciniata NC_068036.1 153221 View on NCBI ↗
Erythranthe lewisii NC_068037.1 153690 View on NCBI ↗
Erythranthe lutea NC_030212.1 153150 View on NCBI ↗
Erythranthe minor NC_068038.1 153175 View on NCBI ↗
Erythranthe nasuta NC_068039.1 153173 View on NCBI ↗
Erythranthe nepalensis NC_077628.1 153625 View on NCBI ↗
Erythranthe nudata NC_068040.1 152817 View on NCBI ↗
Erythranthe pardalis NC_068041.1 153156 View on NCBI ↗
Erythranthe platyphylla NC_077630.1 154268 View on NCBI ↗
Erythranthe szechuanensis NC_077629.1 154274 View on NCBI ↗
Erythranthe tilingii NC_068042.1 153199 View on NCBI ↗