Markers + reference

Trithuria

2 species · Hydatellaceae · Nymphaeales

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Species 2
Genome length 165–179 kb
Candidate markers 289
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 289 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhC-tRNA-Val(UAC) LSC 1104 0.1409 0.92 84.6 yes View details
petA-psbJ LSC 1102 0.1086 0.78 83.1 yes View details
tRNA-Asn(GUU)-ycf1 IRb 486 0.3768 0.99 77.0 yes View details
ycf1 IRb 5202 0.0523 0.99 67.9 yes View details
ndhF-rpl32 SSC 872 0.1532 0.94 83.6 yes View details
rpl32-tRNA-Leu(UAG) SSC 990 0.1815 0.61 74.6 yes View details
ycf1 IRa 5202 0.0523 0.99 67.9 no View details
ycf1-tRNA-Asn(GUU) IRa 486 0.3768 0.99 77.0 yes View details
rps16-tRNA-Gln(UUG) LSC 1134 0.0927 0.92 85.7 yes View details
petN-psbM LSC 1293 0.0852 0.79 82.6 yes View details
psbE-petL LSC 1166 0.0883 0.89 82.6 yes View details
ycf4-cemA LSC 931 0.1064 0.97 82.2 yes View details
tRNA-Thr(UGU)-tRNA-Leu(UAA) LSC 429 0.0909 0.97 81.6 yes View details
tRNA-Thr(GGU)-psbD LSC 1399 0.0662 0.97 81.2 yes View details
ycf3-tRNA-Ser(GGA) LSC 718 0.0876 0.97 80.9 yes View details
tRNA-Ser(UGA)-psbZ LSC 339 0.0683 0.95 80.7 yes View details
tRNA-Ser(GCU)-tRNA-Gly(GCC) LSC 688 0.0752 0.99 80.0 yes View details
tRNA-Phe(GAA)-ndhJ LSC 632 0.0918 0.98 79.7 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
rps16-tRNA-Gln(UUG)_p1 rps16-tRNA-Gln(UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1207–1264 1.000 88.6
rps16-tRNA-Gln(UUG)_p2 rps16-tRNA-Gln(UUG) TCTCATTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 1215–1272 1.000 88.4
rps16-tRNA-Gln(UUG)_p3 rps16-tRNA-Gln(UUG) TGCTTTCTACCGCATCGTTT GAGGTTCGAATCCTTCCGTC 1196–1253 1.000 88.2
rps16-tRNA-Gln(UUG)_p4 rps16-tRNA-Gln(UUG) TTGCTTTCTACCGCATCGTT GAGGTTCGAATCCTTCCGTC 1197–1254 1.000 88.1
rps16-tRNA-Gln(UUG)_p5 rps16-tRNA-Gln(UUG) CTCATTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1214–1271 1.000 87.9
tRNA-Ser(GCU)-tRNA-Gly(GCC)_p1 tRNA-Ser(GCU)-tRNA-Gly(GCC) GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 748–754 1.000 54.9
tRNA-Ser(GCU)-tRNA-Gly(GCC)_p2 tRNA-Ser(GCU)-tRNA-Gly(GCC) AGTCCACTCAGCCATCTCTC ACGAATCACACTTTTACCACT 743–749 1.000 54.1
tRNA-Ser(GCU)-tRNA-Gly(GCC)_p3 tRNA-Ser(GCU)-tRNA-Gly(GCC) GCTTTAGTCCACTCAGCCAT GAACGAATCACACTTTTACCACT 750–756 1.000 53.9
tRNA-Ser(GCU)-tRNA-Gly(GCC)_p4 tRNA-Ser(GCU)-tRNA-Gly(GCC) GCTTTAGTCCACTCAGCCAT AGAACGAATCACACTTTTACCAC 751–757 1.000 53.8
tRNA-Ser(GCU)-tRNA-Gly(GCC)_p5 tRNA-Ser(GCU)-tRNA-Gly(GCC) AGTCCACTCAGCCATCTCTC GAACGAATCACACTTTTACCACT 745–751 1.000 53.0
petN-psbM_p1 petN-psbM AATAAGTCTCGCTTGGGCTG ATTGCTACTGCGCTGTTCAT 1207–1456 1.000 86.9
petN-psbM_p2 petN-psbM GGGGTAGAAGTGGGCTCTAA ATTGCTACTGCGCTGTTCAT 1145–1394 1.000 86.4
petN-psbM_p3 petN-psbM AATAAGTCTCGCTTGGGCTG TATTGCTACTGCGCTGTTCA 1208–1457 1.000 86.0
petN-psbM_p4 petN-psbM TATGGGGTAGAAGTGGGCTC ATTGCTACTGCGCTGTTCAT 1148–1397 1.000 85.8
petN-psbM_p5 petN-psbM GGGGTAGAAGTGGGCTCTAA TATTGCTACTGCGCTGTTCA 1146–1395 1.000 85.5
tRNA-Thr(GGU)-psbD_p1 tRNA-Thr(GGU)-psbD GGCGTAAGTCATCGGTTCAA CAAAAACGAAACGGTCCCTG 1525–1530 1.000 83.6
tRNA-Thr(GGU)-psbD_p2 tRNA-Thr(GGU)-psbD GGCGTAAGTCATCGGTTCAA CACAAAAACGAAACGGTCCC 1527–1532 1.000 83.1
tRNA-Thr(GGU)-psbD_p3 tRNA-Thr(GGU)-psbD GGCGTAAGTCATCGGTTCAA CCACAAAAACGAAACGGTCC 1528–1533 1.000 83.1
tRNA-Thr(GGU)-psbD_p4 tRNA-Thr(GGU)-psbD GGCGTAAGTCATCGGTTCAA CCCACAAAAACGAAACGGTC 1529–1534 1.000 83.1
tRNA-Thr(GGU)-psbD_p5 tRNA-Thr(GGU)-psbD GGCGTAAGTCATCGGTTCAA ACAAAAACGAAACGGTCCCT 1526–1531 1.000 82.5
tRNA-Ser(UGA)-psbZ_p1 tRNA-Ser(UGA)-psbZ CAACCACTCAGCCATCTCTC TGCAAAAACAGCCAATTGGA 376–393 1.000 80.0
tRNA-Ser(UGA)-psbZ_p2 tRNA-Ser(UGA)-psbZ ACGAGCAAAGCAAAAGGAGA TGCAAAAACAGCCAATTGGA 457–474 1.000 78.5
tRNA-Ser(UGA)-psbZ_p3 tRNA-Ser(UGA)-psbZ CAACCACTCAGCCATCTCTC TGCAAAAACAGCCAATTGGAA 376–393 1.000 77.8
tRNA-Ser(UGA)-psbZ_p4 tRNA-Ser(UGA)-psbZ CAACCACTCAGCCATCTCTC AACAGCCAATTGGAAAGCAA 370–387 1.000 77.7
tRNA-Ser(UGA)-psbZ_p5 tRNA-Ser(UGA)-psbZ ACGAGCAAAGCAAAAGGAGA TGCAAAAACAGCCAATTGGAA 457–474 1.000 76.3
ycf3-tRNA-Ser(GGA)_p1 ycf3-tRNA-Ser(GGA) TTGGTAGTCCCCATCCCAAT ACGGCCGTGTAGTGGATATA 1818–1887 1.000 86.4
ycf3-tRNA-Ser(GGA)_p2 ycf3-tRNA-Ser(GGA) TTGGTAGTCCCCATCCCAAT GTTGCGTATGGCTTCCACTA 1883–1952 1.000 86.1
ycf3-tRNA-Ser(GGA)_p3 ycf3-tRNA-Ser(GGA) TTGGTAGTCCCCATCCCAAT TGGCTTCCACTATTCCTGGA 1875–1944 1.000 86.0
ycf3-tRNA-Ser(GGA)_p4 ycf3-tRNA-Ser(GGA) TTGGTAGTCCCCATCCCAAT GCTTCCACTATTCCTGGAGC 1873–1942 1.000 86.0
ycf3-tRNA-Ser(GGA)_p5 ycf3-tRNA-Ser(GGA) TTGGTAGTCCCCATCCCAAT GGAGCCCGCCAATTAGTTAA 1858–1927 1.000 86.0

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
Trithuria inconspicua NC_020372.1 165389 View on NCBI ↗
Trithuria lanterna NC_054150.1 179339 View on NCBI ↗