Markers + reference

Lindenbergia

2 species · Orobanchaceae · Lamiales

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Species 2
Genome length 154–155 kb
Candidate markers 267
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 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
ycf1 SSC 5559 0.3434 0.97 75.7 yes View details
ndhH SSC 1182 0.4315 0.98 81.1 yes View details
ndhD SSC 1506 0.4319 0.99 80.2 yes View details
ccsA SSC 975 0.4415 0.96 82.3 yes View details
ndhF SSC 2259 0.4253 0.98 78.8 yes View details
trnT-UGU-trnL-UAA LSC 729 0.0665 0.95 85.5 yes View details
ycf3-trnS-GGA LSC 749 0.0704 0.97 84.7 yes View details
trnF-GAA-ndhJ LSC 643 0.0986 0.98 84.2 yes View details
trnK-UUU-rps16 LSC 927 0.1018 0.91 83.4 yes View details
trnS-GCU-trnG-UCC LSC 791 0.0798 0.92 83.3 yes View details
trnH-GUG-psbA LSC 561 0.1413 0.97 81.2 yes View details
trnC-GCA-petN LSC 818 0.0750 0.94 81.1 yes View details
trnT-GGU-psbD LSC 1228 0.0644 0.94 81.0 yes View details
ndhC-trnV-UAC LSC 1117 0.0860 0.98 81.0 yes View details
rps16-trnQ-UUG LSC 775 0.0754 0.99 80.6 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA TGTTGGGGCGAATCAGAAAA GAGCTTAGTTTCCGTCTGGG 1623 0.500 59.8
trnH-GUG-psbA_p2 trnH-GUG-psbA TGTTGGGGCGAATCAGAAAA GAGTGGGAGCTTAGTTTCCG 1629 0.500 59.8
trnH-GUG-psbA_p3 trnH-GUG-psbA TGTTGGGGCGAATCAGAAAA GGAGCTTAGTTTCCGTCTGG 1624 0.500 59.8
trnH-GUG-psbA_p4 trnH-GUG-psbA TGTTGGGGCGAATCAGAAAA GGGAGCTTAGTTTCCGTCTG 1625 0.500 59.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GGTTATCCTGCACTCGGAAG GAGCTTAGTTTCCGTCTGGG 1463 0.500 59.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG TTTTCTTGAGCCGTACGAGG 1347–1360 1.000 88.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TTTTCTTGAGCCGTACGAGG 1346–1359 1.000 88.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GCCGTACGAGGAGAAAACTT 1338–1351 1.000 88.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1337–1350 1.000 88.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCCTTTCAGGATCAGTCGT TTTTCTTGAGCCGTACGAGG 1348–1361 1.000 88.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 865–1236 1.000 83.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 848–1219 1.000 83.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 866–1237 1.000 82.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGCACCCTCATTCCTAGACA GAGGTTCGAATCCTTCCGTC 913–1284 1.000 82.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 862–1233 1.000 81.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 824–860 1.000 61.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 823–859 1.000 61.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCTTTAACT 861–897 1.000 61.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCTTTAACT 860–896 1.000 61.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AAACCGAAAGACCCTTTAACT 862–898 1.000 59.9
trnC-GCA-petN_p1 trnC-GCA-petN CGGGTCGTGCTCTATCAAAA CCCAATATATGACTCGCCCG 2037 0.500 59.9
trnC-GCA-petN_p2 trnC-GCA-petN CGGGTCGTGCTCTATCAAAA AATCCGGGCATCGCTAAAAT 1742 0.500 59.8
trnC-GCA-petN_p3 trnC-GCA-petN CGGGTCGTGCTCTATCAAAA AGGTCCGGTTTTCCTCAGTA 1883 0.500 59.8
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CCCAATATATGACTCGCCCG 1435 0.500 59.3
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AATCCGGGCATCGCTAAAAT 1140 0.500 59.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA TTTACCAAGGGCTATAGTCA 1274–1284 1.000 48.6
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TTACCAAGGGCTATAGTCAT 1296–1306 1.000 48.6
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TTTACCAAGGGCTATAGTCA 1297–1307 1.000 48.5
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA TTTACCAAGGGCTATAGTCA 1300–1310 1.000 48.5
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA TTACCAAGGGCTATAGTCAT 1299–1309 1.000 48.5

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
Lindenbergia indica NC_080204.1 154284 View on NCBI ↗
Lindenbergia philippensis NC_022859.1 155103 View on NCBI ↗