Markers + reference

Ruellia

2 species · Acanthaceae · Lamiales

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Species 2
Genome length 149–149 kb
Candidate markers 257
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 405 0.0150 0.99 56.0 yes View details
rps16 LSC 1138 0.0070 1.00 57.8 yes View details
trnS-GCU-trnS-CGA LSC 771 0.0104 1.00 57.2 yes View details
atpH-atpI LSC 1018 0.0060 0.99 53.5 yes View details
rps2 LSC 711 0.0028 1.00 47.0 yes View details
trnC-GCA-petN LSC 844 0.0073 0.97 65.7 yes View details
psaA-ycf3 LSC 696 0.0115 1.00 55.8 yes View details
rpl20-rps12 LSC 780 0.0115 1.00 56.5 yes View details
rpl16 LSC 1249 0.0080 1.00 48.4 yes View details
ycf1 SSC 5451 0.0052 1.00 55.9 yes View details
ndhD SSC 1455 0.0027 1.00 45.4 yes View details
ndhD-ccsA SSC 254 0.0315 1.00 70.6 yes View details
rpl32-ndhF SSC 526 0.0100 0.95 61.8 yes View details
ycf1 IRa 837 0.0024 1.00 46.0 no View details
ycf2-trnH-GUG IRa 87 0.0541 0.85 75.6 no View details
rps19-rpl2 LSC 68 0.0317 0.93 74.6 yes View details
rpl33-rps18 LSC 179 0.0223 1.00 65.3 yes View details
rpl36-infA LSC 95 0.0211 1.00 64.6 yes View details
trnF-GAA-ndhJ LSC 697 0.0086 1.00 63.8 yes View details
rps4-trnT-UGU LSC 489 0.0044 0.93 63.1 yes View details
trnE-UUC-trnT-GGU LSC 615 0.0049 0.99 62.4 yes View details
trnR-ACG-trnN-GUU IRb 563 0.0054 0.99 62.3 yes View details
trnN-GUU-trnR-ACG IRa 563 0.0054 0.99 62.3 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 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 CGTGCTAACCTTGGTATGGA 519–521 1.000 75.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGTGCTAACCTTGGTATGG 520–522 1.000 75.3
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CGTGCTAACCTTGGTATGGA 533–535 1.000 75.3
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGTGCTAACCTTGGTATGG 534–536 1.000 75.3
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CGTGCTAACCTTGGTATGGA 532–534 1.000 75.3
rps16_p1 rps16 AAAAGAATACAGCGGAGGGG CCGGTTCCAAATTCGAGGAA 1254–1256 1.000 75.7
rps16_p2 rps16 AAAAGAATACAGCGGAGGGG ATGGACAACCGAAGCAATGA 1308–1310 1.000 75.5
rps16_p3 rps16 AAAAGAATACAGCGGAGGGG GTCTATGGACAACCGAAGCA 1312–1314 1.000 74.1
rps16_p4 rps16 AAAAGAATACAGCGGAGGGG TACCGGTTCCAAATTCGAGG 1256–1258 1.000 74.0
rps16_p5 rps16 AAAAGAATACAGCGGAGGGG GGACAACCGAAGCAATGACT 1306–1308 1.000 73.3
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA ACCACTAAACTACACCCGCT 826–836 1.000 75.6
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC ACCACTAAACTACACCCGCT 825–835 1.000 75.6
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA ACGGAAAGAGAGGGATTCGA ACCACTAAACTACACCCGCT 880–890 1.000 74.4
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AGCAATCCGACGCTTTAGTC ACCACTAAACTACACCCGCT 828–838 1.000 72.8
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CGACGCTTTAGTCCACTCAG ACCACTAAACTACACCCGCT 821–831 1.000 72.6
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1142–1152 1.000 78.3
atpH-atpI_p2 atpH-atpI GTCCAATAGAAGCAAGCCCT TCCCTGTCATGTTCCTTGGA 1182–1192 1.000 75.7
atpH-atpI_p3 atpH-atpI AACGGAAGCAGCAGAAATCA TAGGTGAATCCATGGAGGGT 1067–1077 1.000 75.7
atpH-atpI_p4 atpH-atpI AACGGAAGCAGCAGAAATCA AGTGGTTCCTATCCCTGTCA 1153–1163 1.000 75.2
atpH-atpI_p5 atpH-atpI AACGGAAGCAGCAGAAATCA TCAGTGGTTCCTATCCCTGT 1155–1165 1.000 75.2
rps2_p1 rps2 ACGTGAGTAAAGCCAAAGCA GGGTCGAATCGATTGGTTGA 1831–1834 1.000 80.0
rps2_p2 rps2 CAAGGGCCGTATTCTTCTCC GGGTCGAATCGATTGGTTGA 1679–1682 1.000 80.0
rps2_p3 rps2 CCAAGGGCCGTATTCTTCTC GGGTCGAATCGATTGGTTGA 1680–1683 1.000 80.0
rps2_p4 rps2 GGAAACCCCCTATTTGCCAA GGGTCGAATCGATTGGTTGA 1498–1501 1.000 79.9
rps2_p5 rps2 TTGGAAACCCCCTATTTGCC GGGTCGAATCGATTGGTTGA 1500–1503 1.000 79.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 935–954 1.000 81.8
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 933–952 1.000 81.8
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 936–955 1.000 81.2
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 881–900 1.000 80.8
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTCTTCCCCACACTACGAGT 951–970 1.000 79.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Ruellia elegans NC_082429.1 149384 View on NCBI ↗
Ruellia speciosa NC_080332.1 148941 View on NCBI ↗