Markers + reference

Ottelia

19 species · Hydrocharitaceae · Alismatales

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Species 19
Genome length 156–158 kb
Candidate markers 269
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 614 0.0206 1.00 69.8 yes View details
rps16-trnQ-UUG LSC 843 0.0203 1.00 69.3 yes View details
trnS-GCU-trnG-UCC LSC 951 0.0231 0.98 78.5 yes View details
rpoB-trnC-GCA LSC 1208 0.0163 1.00 66.3 yes View details
petN-psbM LSC 1338 0.0209 0.98 65.6 yes View details
trnT-UGU-trnL-UAA LSC 894 0.0197 1.00 68.8 yes View details
ndhC-trnV-UAC LSC 1250 0.0203 0.99 71.4 yes View details
petA-psbJ LSC 954 0.0200 1.00 62.0 yes View details
rpl16 LSC 1474 0.0153 0.98 59.5 yes View details
rps19 LSC 279 0.0114 1.00 35.7 yes View details
ccsA SSC 969 0.0084 1.00 46.6 yes View details
rps19-rpl2 IRb 78 0.0393 1.00 67.2 yes View details
ccsA-ndhD SSC 230 0.0496 1.00 66.9 yes View details
trnN-GUU-ndhF IRb 610 0.0102 0.98 65.2 yes View details
ycf3-trnS-GGA LSC 647 0.0148 1.00 64.9 yes View details
trnH-GUG-psbA LSC 267 0.0192 1.00 63.8 yes View details
psaJ-rpl33 LSC 406 0.0233 1.00 63.5 yes View details
rpl22-rps19 LSC 326 0.0252 0.98 62.9 yes View details
ycf4-cemA LSC 992 0.0169 1.00 62.8 yes View details
ndhF-rpl32 SSC 669 0.0160 0.99 62.7 yes View details
rpl32-trnL-UAG SSC 637 0.0147 0.97 62.6 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 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 CAATCCACCGCCTTAATCCA GTAACGCTCACAACTTCCCT 351–365 1.000 88.7
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACCGCCTTAATCCAC GTAACGCTCACAACTTCCCT 350–364 1.000 88.7
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACCGCCTTAATCC GTAACGCTCACAACTTCCCT 352–366 1.000 88.6
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACCGCCTTAATCCA CAACCGTGCTAACCTTGGTA 389–403 1.000 88.2
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACCGCCTTAATCCAC CAACCGTGCTAACCTTGGTA 388–402 1.000 88.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGGGCTCAACCTACAGAAAC 733–799 1.000 85.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGGGCTCAACCTACAGAAAC 732–798 1.000 85.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACAGAAACGGT 729–795 0.947 83.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACCTACAGAAACGGT 730–796 0.947 82.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GCTCAACCTACAGAAACGGT 739–805 0.947 81.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGGTCCTGTTATTCGGAGGT 891–989 1.000 88.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 876–974 1.000 88.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 880–978 1.000 83.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TGGTCCTGTTATTCGGAGGT 883–981 1.000 83.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 868–966 1.000 83.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAACAAAACTGAAAGACCCCT 1050–1098 0.895 71.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAACAAAACTGAAAGACCCCT 1049–1097 0.895 71.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GATCAGAGGGAACGGAGAGA TGAACAAAACTGAAAGACCCCT 1115–1162 0.842 67.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATCAGAGGGAACGGAGAGAG TGAACAAAACTGAAAGACCCCT 1114–1161 0.842 67.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CTCAAGCGATCAGAGGGAAC TGAACAAAACTGAAAGACCCCT 1122–1169 0.842 67.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ACTCTTCTGTCAAGCCCTGA GCGACACCCAGATTTGAACT 1370–1409 1.000 80.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ACTCTTCTGTCAAGCCCTGA TAAAGGATTTGCAGTCCCCC 1345–1384 1.000 79.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ACTCTTCTGTCAAGCCCTGA CCTTACCACTTGGCCATGTC 1324–1363 1.000 79.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ACTCTTCTGTCAAGCCCTGA TATTGAGCTGATCAGGCGAC 1385–1424 1.000 79.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AACTCTTCTGTCAAGCCCTG GCGACACCCAGATTTGAACT 1371–1410 1.000 77.8
petN-psbM_p1 petN-psbM CGGTATCGGTTTTGGCTACA TTTTATTGGTTGGATGCGCG 2401–2542 0.684 72.2
petN-psbM_p2 petN-psbM CTCTGCTCCTATTGGCCAAG TTTTATTGGTTGGATGCGCG 2292–2433 0.684 72.0
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TTTTATTGGTTGGATGCGCG 1881–2034 0.684 71.1
petN-psbM_p4 petN-psbM AGTAGGTAGGGGTATTCCGC TTTTATTGGTTGGATGCGCG 2157–2300 0.421 59.3
petN-psbM_p5 petN-psbM AGTAGGTAGGGGTATTCCGC CGCGAGCAATGGAATAGGAA 2141–2284 0.421 58.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (19)

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

Species Accession Length (bp) Link
Ottelia acuminata NC_060997.1 156995 View on NCBI ↗
Ottelia acuminata var. acuminata MT241428.1 156995 View on NCBI ↗
Ottelia acuminata var. crispa MT241445.1 156981 View on NCBI ↗
Ottelia acuminata var. jingxiensis NC_060998.1 156816 View on NCBI ↗
Ottelia acuminata var. lunanensis NC_060999.1 156908 View on NCBI ↗
Ottelia acuminata var. songmingensis NC_061000.1 157646 View on NCBI ↗
Ottelia balansae NC_061001.1 156945 View on NCBI ↗
Ottelia brasiliensis MT241422.1 157486 View on NCBI ↗
Ottelia cordata NC_046891.1 157869 View on NCBI ↗
Ottelia cylindrica MT241421.1 157175 View on NCBI ↗
Ottelia emersa NC_061002.1 157896 View on NCBI ↗
Ottelia fengshanensis NC_061003.1 157457 View on NCBI ↗
Ottelia fischeri MT241412.1 156816 View on NCBI ↗
Ottelia guanyangensis NC_061004.1 157362 View on NCBI ↗
Ottelia mesenterium NC_061005.1 157824 View on NCBI ↗
Ottelia muricata MT241420.1 156810 View on NCBI ↗
Ottelia ovalifolia MT241423.1 157694 View on NCBI ↗
Ottelia ulvifolia MT241417.1 157847 View on NCBI ↗
Ottelia verdickii MT241416.1 156433 View on NCBI ↗