Markers + reference

Utricularia

25 species · Lentibulariaceae · Lamiales

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Species 25
Genome length 132–154 kb
Candidate markers 258
Primer pairs 85

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 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 883 0.2066 0.89 77.1 yes View details
rps16-trnQ-UUG LSC 514 0.1973 0.89 74.3 yes View details
trnS-GCU-trnG-UCC LSC 646 0.2159 0.91 81.0 yes View details
rpoB-trnC-GCA LSC 1151 0.1859 0.95 80.3 yes View details
ycf1 SSC 438 0.0529 1.00 75.8 no View details
rpl32-trnL-UAG SSC 504 0.2662 0.91 74.2 yes View details
rps15-ycf1 SSC 306 0.2442 0.89 71.0 yes View details
ycf1 SSC 4629 0.1561 0.98 78.5 yes View details
trnT-GGU-psbD LSC 1336 0.1294 0.98 86.2 yes View details
atpB-rbcL LSC 759 0.1018 0.97 84.4 yes View details
matK-trnK-UUU LSC 692 0.1011 0.99 83.6 yes View details
rpl20-rps12 LSC 802 0.0949 0.97 83.6 yes View details
accD LSC 1512 0.0650 1.00 83.3 yes View details
ccsA SSC 969 0.1005 1.00 83.3 yes View details
rps16 LSC 1095 0.1030 0.99 82.7 yes View details
petB LSC 1390 0.0669 0.98 82.7 yes View details
rpoA LSC 1068 0.0709 0.99 82.7 yes View details
rbcL-accD LSC 661 0.1304 0.94 82.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU TTGCAATTCCAAGACTCGCT CGTGATAACGGAACAGGGTT 1656 0.040 40.1
matK-trnK-UUU_p2 matK-trnK-UUU TTGCAATTCCAAGACTCGCT TCGGGTTGCTAACTCAATGG 1282 0.040 39.9
matK-trnK-UUU_p3 matK-trnK-UUU TTGCAATTCCAAGACTCGCT GGAACAGGGTTGCGTCTATT 1647 0.040 39.9
matK-trnK-UUU_p4 matK-trnK-UUU TTGCAATTCCAAGACTCGCT CGGGTTGCTAACTCAATGGT 1281 0.040 39.3
matK-trnK-UUU_p5 matK-trnK-UUU TTGCAATTCCAAGACTCGCT TGATAACGGAACAGGGTTGC 1654 0.040 39.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AACGGCAGGCAATAGTTAGG AAAAGGGTATGTTGCTGCCA 1876–2065 0.640 77.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AACGGCAGGCAATAGTTAGG TCGATCTCGACGAGAAGGAA 1481–1571 0.440 69.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TTACACATAGAACGGCAGGC AAAAGGGTATGTTGCTGCCA 2019–2076 0.160 58.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTACACATAGAACGGCAGGC TCGATCTCGACGAGAAGGAA 1535–1561 0.120 56.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TTACACATAGAACGGCAGGC TAGTCAACGTGGATCATGCG 2081 0.040 40.8
rps16_p1 rps16 AACCCTGTTCCGTTATCACG CTACTGTGTACCGCTGAACC 1705 0.040 40.8
rps16_p2 rps16 AATAGACGCAACCCTGTTCC CTACTGTGTACCGCTGAACC 1714 0.040 40.7
rps16_p3 rps16 AACCCTGTTCCGTTATCACG GAGGTTCGAATCCTTCCGTC 2160 0.040 40.3
rps16_p4 rps16 AACCCTGTTCCGTTATCACG GTACCGCTGAACCAATGACT 1698 0.040 40.1
rps16_p5 rps16 AATAGACGCAACCCTGTTCC GAGGTTCGAATCCTTCCGTC 2169 0.040 40.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGGCAGCAACATACCCTTTT CTTACAGCTGCTTGCCAAAC 1382–1891 0.760 81.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGGCAGCAACATACCCTTTT GAGGTTCGAATCCTTCCGTC 829–1294 0.720 80.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGATCCTTGTCCCCGAGAAA CTTACAGCTGCTTGCCAAAC 1200–1688 0.640 76.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGCATCCTCATTTCGCGATT CTTACAGCTGCTTGCCAAAC 1243 0.040 40.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGCATCCTCATTTCGCGATT GAGGTTCGAATCCTTCCGTC 654 0.040 40.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 622–1175 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 624–1177 1.000 62.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 623–1176 0.960 62.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 626–1179 0.960 61.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 625–1178 0.960 61.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TTTTCTACTAACGCGAGCCC TTGCAAGCCTTGGTCTTGAT 1976 0.040 41.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATACTGGATCCCCACCTACG TTGCAAGCCTTGGTCTTGAT 2166 0.040 41.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCACCTACGCAAGCAAATTG TTGCAAGCCTTGGTCTTGAT 2155 0.040 41.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TTGCAAGCCTTGGTCTTGAT 1963 0.040 41.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCTACTAACGCGAGCCCATA TTGCAAGCCTTGGTCTTGAT 1973 0.040 41.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (25)

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

Species Accession Length (bp) Link
Utricularia adpressa MZ981773.1 133386 View on NCBI ↗
Utricularia arenaria OK187459.1 150914 View on NCBI ↗
Utricularia aurea NC_084257.1 150602 View on NCBI ↗
Utricularia australis OK187460.1 153978 View on NCBI ↗
Utricularia cucullata OK187461.1 142119 View on NCBI ↗
Utricularia flaccida OK187462.1 149260 View on NCBI ↗
Utricularia foliosa KY025562.1 150851 View on NCBI ↗
Utricularia geminiloba OK187463.1 139075 View on NCBI ↗
Utricularia graminifolia OK187465.1 141492 View on NCBI ↗
Utricularia hispida OK187466.1 151780 View on NCBI ↗
Utricularia intermedia NC_084258.1 152474 View on NCBI ↗
Utricularia longifolia OK187467.1 151121 View on NCBI ↗
Utricularia minor NC_084259.1 153707 View on NCBI ↗
Utricularia nelumbifolia OK187468.1 138307 View on NCBI ↗
Utricularia neottioides OK187469.1 146626 View on NCBI ↗
Utricularia nephrophylla OK187470.1 138861 View on NCBI ↗
Utricularia olivacea OK187471.1 131501 View on NCBI ↗
Utricularia pubescens OK187472.1 148408 View on NCBI ↗
Utricularia simulans OK187473.1 140095 View on NCBI ↗
Utricularia subulata OK187474.1 149119 View on NCBI ↗
Utricularia tenuicaulis NC_058517.1 154021 View on NCBI ↗
Utricularia tricolor OK187475.1 149830 View on NCBI ↗
Utricularia triloba OK187476.1 148378 View on NCBI ↗
Utricularia volubilis OK187477.1 143459 View on NCBI ↗
Utricularia vulgaris NC_084260.1 151986 View on NCBI ↗