Markers + reference

Muellerina

2 species · Loranthaceae · Santalales

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Species 2
Genome length 123–127 kb
Candidate markers 209
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 209 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0019 1.00 48.2 yes View details
psbA-matK LSC 548 0.0244 0.97 60.0 yes View details
matK-trnQ-CAA LSC 1585 0.0209 0.66 56.2 yes View details
trnS-AGC-trnR-AGA LSC 471 0.0523 0.93 80.8 yes View details
ycf3-trnS-UCC LSC 693 0.0189 0.92 66.5 yes View details
rbcL-accD LSC 466 0.0210 0.92 60.0 yes View details
psaC-ycf1 SSC 1088 0.0234 0.98 63.9 yes View details
ycf1 SSC 4104 0.0184 1.00 50.2 yes View details
trnY-UAC-trnE-GAA LSC 57 0.0526 1.00 73.4 yes View details
psbZ-trnG-GGC LSC 267 0.0243 0.93 70.4 yes View details
ycf15-trnL-UUG IRb 544 0.0149 0.99 67.6 yes View details
trnL-UUG-ycf15 IRa 544 0.0149 0.99 67.6 yes View details
ccsA-psaC SSC 314 0.0317 0.90 67.1 yes View details
atpB-rbcL LSC 596 0.0119 0.99 66.8 yes View details
rpoA-rps11 LSC 67 0.0317 0.94 66.8 yes View details
rps4-trnT-ACA LSC 358 0.0224 1.00 65.9 yes View details
psaJ-rpl33 LSC 91 0.0330 1.00 63.9 yes View details
rps12-trnV-GUC IRb 1804 0.0083 1.00 63.1 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA GCTCCTTTACTTTCAAGAACTCA TCATGCTTGGGAGTCTCTGA 1149 0.500 25.4
psbA_p2 psbA GCTCCTTTACTTTCAAGAACTCA TGCTTGGGAGTCTCTGATGA 1146 0.500 25.4
psbA_p3 psbA TGCTCCTTTACTTTCAAGAACTC TCATGCTTGGGAGTCTCTGA 1150 0.500 25.4
psbA_p4 psbA TGCTCCTTTACTTTCAAGAACTC TGCTTGGGAGTCTCTGATGA 1147 0.500 25.4
psbA_p5 psbA TGCTCCTTTACTTTCAAGAACTCA TGCTTGGGAGTCTCTGATGA 1147 0.500 25.0
psbA-matK_p1 psbA-matK GGAGCAGCAATGAAGGCTAT ACAGTTCCAATTCGGCCTTT 1129–1144 1.000 82.3
psbA-matK_p2 psbA-matK CGCCGTTGTATAACCACTCA ACAGTTCCAATTCGGCCTTT 1290–1305 1.000 82.1
psbA-matK_p3 psbA-matK AAGGACCGCCGTTGTATAAC ACAGTTCCAATTCGGCCTTT 1296–1311 1.000 82.0
psbA-matK_p4 psbA-matK CTACTGGAGGAGCAGCAATG ACAGTTCCAATTCGGCCTTT 1137–1152 1.000 82.0
psbA-matK_p5 psbA-matK CGCCGTTGTATAACCACTCA AATTCGGCCTTTGGTTGGAT 1282–1297 1.000 81.7
matK-trnQ-CAA_p1 matK-trnQ-CAA TCCCTGTTTACGAGTTCGATC GGCGTAGTCAAGTGGTAAGG 1185–1705 1.000 73.2
matK-trnQ-CAA_p2 matK-trnQ-CAA TCCCTGTTTACGAGTTCGATC GGGCGTAGTCAAGTGGTAAG 1186–1706 1.000 73.2
matK-trnQ-CAA_p3 matK-trnQ-CAA CCCTGTTTACGAGTTCGATCT GGCGTAGTCAAGTGGTAAGG 1184–1704 1.000 73.1
matK-trnQ-CAA_p4 matK-trnQ-CAA CCCTGTTTACGAGTTCGATCT GGGCGTAGTCAAGTGGTAAG 1185–1705 1.000 73.1
matK-trnQ-CAA_p5 matK-trnQ-CAA TCCCTGTTTACGAGTTCGATC AATTGAAGTGGGGCGTAGTC 1196–1716 1.000 72.3
trnS-AGC-trnR-AGA_p1 trnS-AGC-trnR-AGA ATTAGCAATCCGCCGCTTTA AGAAGACCTCTGTCCTATCCA 532–547 1.000 70.7
trnS-AGC-trnR-AGA_p2 trnS-AGC-trnR-AGA GAAAGAGGGGGATTCGAACC AGAAGACCTCTGTCCTATCCA 578–593 1.000 70.4
trnS-AGC-trnR-AGA_p3 trnS-AGC-trnR-AGA GGAAAGAGGGGGATTCGAAC AGAAGACCTCTGTCCTATCCA 579–594 1.000 70.4
trnS-AGC-trnR-AGA_p4 trnS-AGC-trnR-AGA ATTAGCAATCCGCCGCTTTA AGGTTTAGAAGACCTCTGTCCT 538–553 1.000 70.0
trnS-AGC-trnR-AGA_p5 trnS-AGC-trnR-AGA GAAAGAGGGGGATTCGAACC AGGTTTAGAAGACCTCTGTCCT 584–599 1.000 69.7
trnY-UAC-trnE-GAA_p1 trnY-UAC-trnE-GAA ATTTGAACCAGCGTAGGCAT ATGATGTAGGTATGCCCCCA 214 1.000 79.0
trnY-UAC-trnE-GAA_p2 trnY-UAC-trnE-GAA ATTTGAACCAGCGTAGGCAT TGATGTAGGTATGCCCCCAT 213 1.000 79.0
trnY-UAC-trnE-GAA_p3 trnY-UAC-trnE-GAA ATTTGAACCAGCGTAGGCAT CTCTCTTTCAAGGAGGCAGC 173 1.000 78.3
trnY-UAC-trnE-GAA_p4 trnY-UAC-trnE-GAA ATTTGAACCAGCGTAGGCAT TCGTCTAGTGGTTCAGGACA 194 1.000 78.0
trnY-UAC-trnE-GAA_p5 trnY-UAC-trnE-GAA CAACGAATTTACAGTCCGCC TGATGTAGGTATGCCCCCAT 188 1.000 76.1
psbZ-trnG-GGC_p1 psbZ-trnG-GGC TCCCGATGGTTGGTCAAGTA CCTTCTCCTTGGCAAAGAGG 403–415 1.000 80.9
psbZ-trnG-GGC_p2 psbZ-trnG-GGC TTTGCTTCTCCCGATGGTTG CCTTCTCCTTGGCAAAGAGG 411–423 1.000 79.9
psbZ-trnG-GGC_p3 psbZ-trnG-GGC CCCGATGGTTGGTCAAGTAA CCTTCTCCTTGGCAAAGAGG 402–414 1.000 79.9
psbZ-trnG-GGC_p4 psbZ-trnG-GGC ATTTGCTTCTCCCGATGGTT CCTTCTCCTTGGCAAAGAGG 412–424 1.000 79.5
psbZ-trnG-GGC_p5 psbZ-trnG-GGC TTCTCCCGATGGTTGGTCAA CCTTCTCCTTGGCAAAGAGG 406–418 1.000 76.2

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
Muellerina celastroides NC_084057.1 126675 View on NCBI ↗
Muellerina eucalyptoides NC_084058.1 122767 View on NCBI ↗