Markers + reference

Anna

4 species · Gesneriaceae · Lamiales

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Species 4
Genome length 154–154 kb
Candidate markers 273
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 337 0.0160 0.98 58.5 yes View details
atpF-atpH LSC 350 0.0100 1.00 37.1 yes View details
cemA LSC 693 0.0026 1.00 39.0 yes View details
petD LSC 1240 0.0078 1.00 39.8 yes View details
ycf1 IRb 735 0.0075 1.00 60.2 yes View details
ndhF SSC 2217 0.0031 1.00 45.8 yes View details
rpl32-trnL-UAG SSC 854 0.0090 1.00 51.2 yes View details
psaC SSC 246 0.0000 1.00 20.0 yes View details
rps15-ycf1 SSC 391 0.0043 1.00 33.6 yes View details
ycf1 SSC 5484 0.0060 1.00 42.8 yes View details
ndhD-psaC SSC 96 0.0434 1.00 82.4 yes View details
atpH-atpI LSC 1055 0.0046 1.00 60.8 yes View details
psbK-psbI LSC 423 0.0047 1.00 57.9 yes View details
psaI-ycf4 LSC 430 0.0035 1.00 57.9 yes View details
ndhG-ndhI SSC 342 0.0068 1.00 57.9 yes View details
petN-psbM LSC 1007 0.0048 1.00 57.2 yes View details
ycf4-cemA LSC 873 0.0053 1.00 56.9 yes View details
psbT-psbN LSC 65 0.0410 1.00 56.8 yes View details
rps2-rpoC2 LSC 203 0.0092 0.97 56.6 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 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 CCGTGCTAACCTTGGTATGG 444–452 1.000 80.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 458–466 1.000 80.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 457–465 1.000 80.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 459–467 1.000 80.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 445–453 1.000 79.7
trnK-UUU_p1 trnK-UUU TTCGTGTCAACCAATCCCAA ACCCTTTGTTGAGATTATGT 2728–2730 1.000 40.9
trnK-UUU_p2 trnK-UUU TTCGTGTCAACCAATCCCAA ACCCTTTGTTGAGATTATGTT 2728–2730 1.000 40.9
trnK-UUU_p3 trnK-UUU TTCGTGTCAACCAATCCCAA ACCCTTTGTTGAGATTATGTTT 2728–2730 1.000 40.9
trnK-UUU_p4 trnK-UUU TCGTGTCAACCAATCCCAAT ACCCTTTGTTGAGATTATGT 2727–2729 1.000 40.9
trnK-UUU_p5 trnK-UUU TCGTGTCAACCAATCCCAAT ACCCTTTGTTGAGATTATGTT 2727–2729 1.000 40.9
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT GGATTACGTCCCGGATCATT 552–553 1.000 73.6
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGTCCCGGATCATT 547–548 1.000 73.6
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT TCTTCACGTCCAGGATTACG 564–565 1.000 72.8
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 559–560 1.000 72.8
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGATTACGTCCCGGATCATT 544–545 1.000 71.6
atpF-atpH_p1 atpF-atpH AACAACTCACACACACTCCC GTCCTTTCGTCTCGTTTCGA 1068–1088 1.000 80.2
atpF-atpH_p2 atpF-atpH AACAACTCACACACACTCCC TCCTTTCGTCTCGTTTCGAC 1067–1087 1.000 80.2
atpF-atpH_p3 atpF-atpH AACAACTCACACACACTCCC AGTCCTTTCGTCTCGTTTCG 1069–1089 1.000 80.2
atpF-atpH_p4 atpF-atpH AACAACTCACACACACTCCC CCTTTCGTCTCGTTTCGACT 1066–1086 1.000 80.2
atpF-atpH_p5 atpF-atpH CACACACACTCCCTTTCCAA TCCTTTCGTCTCGTTTCGAC 1060–1080 1.000 80.1
atpH-atpI_p1 atpH-atpI TCCGATAGAAGCAAGCCCTA AGTGGTTCCCATACCTGTCA 1228–1239 1.000 80.4
atpH-atpI_p2 atpH-atpI TCCGATAGAAGCAAGCCCTA TCAGTGGTTCCCATACCTGT 1230–1241 1.000 80.4
atpH-atpI_p3 atpH-atpI AACGGAAGCAGCAGAAATCA AGTGGTTCCCATACCTGTCA 1189–1200 1.000 80.3
atpH-atpI_p4 atpH-atpI AACGGAAGCAGCAGAAATCA TCAGTGGTTCCCATACCTGT 1191–1202 1.000 80.3
atpH-atpI_p5 atpH-atpI TCCAGGTCCGATAGAAGCAA AGTGGTTCCCATACCTGTCA 1234–1245 1.000 79.9
rps2-rpoC2_p1 rps2-rpoC2 CCAGCATCTCTTCCAAGGTG TTCGAGGGGGAAATGAGAGA 356–363 1.000 78.5
rps2-rpoC2_p2 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TTCGAGGGGGAAATGAGAGA 359–366 1.000 77.8
rps2-rpoC2_p3 rps2-rpoC2 CTCCAGCATCTCTTCCAAGG TTCGAGGGGGAAATGAGAGA 358–365 1.000 77.8
rps2-rpoC2_p4 rps2-rpoC2 TCCAGCATCTCTTCCAAGGT TTCGAGGGGGAAATGAGAGA 357–364 1.000 77.8
rps2-rpoC2_p5 rps2-rpoC2 CCAGCATCTCTTCCAAGGTG TCGAGGGGGAAATGAGAGAT 355–362 1.000 76.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Anna mollifolia NC_077643.1 154047 View on NCBI ↗
Anna ophiorrhizoides NC_077644.1 154144 View on NCBI ↗
Anna rubidiflora NC_077645.1 154150 View on NCBI ↗
Anna submontana NC_077646.1 154056 View on NCBI ↗