Markers + reference

Ceratostigma

3 species · Plumbaginaceae · Caryophyllales

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Species 3
Genome length 165–165 kb
Candidate markers 261
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf3 LSC 2403 0.0169 0.96 61.8 yes View details
ycf3-accD LSC 972 0.0695 0.89 80.4 yes View details
accD LSC 2676 0.0552 0.91 74.6 yes View details
ycf1 IRb 7548 0.0060 0.98 43.7 no View details
ycf1 IRa 7548 0.0072 0.99 45.1 yes View details
ycf2-trnI-CAU IRa 328 0.0081 1.00 50.7 yes View details
trnI-CAU-trnH-GUG IRa 276 0.0453 0.99 74.7 no View details
ccsA-ndhD SSC 227 0.0413 1.00 73.3 yes View details
trnS-GCU-trnG-UCC LSC 960 0.0163 0.98 72.3 yes View details
ndhF-rpl32 SSC 1097 0.0177 0.98 71.9 yes View details
trnK-UUU-rps16 LSC 1321 0.0066 0.99 65.0 yes View details
atpH-atpI LSC 717 0.0065 1.00 64.2 yes View details
rpl33-rps18 LSC 380 0.0080 0.99 64.2 yes View details
rpl2-trnI-CAU LSC 1288 0.0117 0.98 63.6 yes View details
rps16-trnQ-UUG LSC 593 0.0056 1.00 63.0 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AACTCTACCGATGGTGTGGA TCTTGAAAAGGGTGCTCAACC 1496–1510 1.000 68.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTGTGGACAAATCCT TCTTGAAAAGGGTGCTCAACC 1488–1502 1.000 67.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACCGATGGTGTGGACAAATC TCTTGAAAAGGGTGCTCAACC 1490–1504 1.000 67.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AACTCTACCGATGGTGTGGA TCTTGAAAAGGGTGCTCAAC 1496–1510 1.000 66.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTGTGGACAAATCCT TCTTGAAAAGGGTGCTCAAC 1488–1502 1.000 66.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCCACACCAGATCATGTCCT TTTGGTCCCGCTATTCGAAG 705–1215 1.000 80.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCACACCAGATCATGTCCT TACATTTTAGTGGGGCGTGG 746–1256 1.000 79.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCCACACCAGATCATGTCCT GTTTTGGTCCCGCTATTCGA 707–1217 1.000 78.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACACACGTTGCTTTCTACCA TTTGGTCCCGCTATTCGAAG 680–1190 1.000 78.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACACGTTGCTTTCTACCACA TTTGGTCCCGCTATTCGAAG 678–1188 1.000 78.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATTGGGGATCTAACCGAGGC 1098–1135 1.000 73.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CGAATCACTCGTACAACGGA ATTGGGGATCTAACCGAGGC 1068–1105 1.000 72.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AATTGGGGATCTAACCGAGG 1099–1136 1.000 72.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGAATCACTCGTACAACGGA AATTGGGGATCTAACCGAGG 1069–1106 1.000 71.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AAATTGGGGATCTAACCGAGG 1100–1137 1.000 70.6
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA ACAAGTGGTATCCAGGCTCT 821–825 1.000 80.3
atpH-atpI_p2 atpH-atpI AACAGAAGCGGCAGAAATCA ATAGGGGAATCCATGGAGGG 773–777 1.000 80.2
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ACAAGTGGTATCCAGGCTCT 879–883 1.000 80.1
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 831–835 1.000 80.0
atpH-atpI_p5 atpH-atpI AGCCAATCCAGCAGCAATAA ACAAGTGGTATCCAGGCTCT 839–843 1.000 79.9
ycf3_p1 ycf3 TCCCACGAGAGGTAATGAGA TGATTGATTGGCTCTTCCCG 2458–2510 1.000 78.9
ycf3_p2 ycf3 TCCCACGAGAGGTAATGAGA GATTGGCTCTTCCCGGAATT 2453–2505 1.000 78.8
ycf3_p3 ycf3 TCCCACGAGAGGTAATGAGA TTGGCTCTTCCCGGAATTTT 2451–2503 1.000 76.9
ycf3_p4 ycf3 TCCCACGAGAGGTAATGAGAA TGATTGATTGGCTCTTCCCG 2458–2510 1.000 76.7
ycf3_p5 ycf3 TTCCCACGAGAGGTAATGAGA TGATTGATTGGCTCTTCCCG 2459–2511 1.000 76.7
ycf3-accD_p1 ycf3-accD TGAAATTGCAGAGGCTTGGT GGGGAGTTGTTGGGACTTTT 1235–1299 1.000 89.9
ycf3-accD_p2 ycf3-accD TGAAACTCATGCACCTTGCT GGGGAGTTGTTGGGACTTTT 1442–1502 1.000 89.0
ycf3-accD_p3 ycf3-accD TGAAATTGCAGAGGCTTGGT GGGAATTGCTAGGGGAGTTG 1278–1310 0.667 75.8
ycf3-accD_p4 ycf3-accD TGAAACTCATGCACCTTGCT GGGAATTGCTAGGGGAGTTG 1485–1513 0.667 75.0
ycf3-accD_p5 ycf3-accD GCTGAAGGTGGGACAAAAGA GGGAATTGCTAGGGGAGTTG 1549–1577 0.667 74.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Ceratostigma minus NC_071214.1 164789 View on NCBI ↗
Ceratostigma plumbaginoides NC_071212.1 164744 View on NCBI ↗
Ceratostigma willmottianum NC_041261.1 164999 View on NCBI ↗