Markers + reference

Alisma

7 species · Alismataceae · Alismatales

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Species 7
Genome length 160–160 kb
Candidate markers 267
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1724 0.0036 1.00 42.4 yes View details
trnS-GCU-psbI LSC 227 0.0204 0.99 47.5 yes View details
trnE-UUC-trnT-GGU LSC 671 0.0060 1.00 45.2 yes View details
trnT-UGU-trnL-UAA LSC 1114 0.0054 0.99 55.8 yes View details
ndhC LSC 363 0.0000 1.00 26.8 yes View details
ndhC-trnV-UAC LSC 1475 0.0048 1.00 63.9 yes View details
psbE-petL LSC 1225 0.0050 1.00 46.4 yes View details
petD LSC 1274 0.0038 1.00 51.3 yes View details
trnN-GUU-ndhF IRb 952 0.0355 1.00 80.7 yes View details
rpl32-trnL-UAG SSC 386 0.0104 1.00 47.6 yes View details
ccsA-ndhD SSC 262 0.0142 1.00 38.3 yes View details
ndhG-ndhI SSC 657 0.0067 1.00 46.0 yes View details
ycf1 SSC 5307 0.0037 1.00 36.4 yes View details
trnQ-UUG-trnG-UCC LSC 1124 0.0041 1.00 64.0 yes View details
psbZ-trnG-GCC LSC 753 0.0051 1.00 58.8 yes View details
trnT-GGU-psbD LSC 1151 0.0034 1.00 54.8 yes View details
atpF-atpH LSC 573 0.0013 0.99 54.7 yes View details
accD-psaI LSC 901 0.0040 1.00 53.6 yes View details
clpP LSC 2073 0.0011 1.00 53.3 yes View details
rps16-trnS-GCU LSC 1017 0.0051 1.00 51.1 yes View details
rpl16 LSC 1428 0.0013 1.00 51.1 yes View details
atpH-atpI LSC 993 0.0036 1.00 50.8 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 CCTTTCAGGATCAGTCGTGG GGCGTTCTGTCTATCCATGG 2515–2544 1.000 80.0
rps16_p2 rps16 CCTTTCAGGATCAGTCGTGG GGGCGTTCTGTCTATCCATG 2516–2545 1.000 80.0
rps16_p3 rps16 CCTTTCAGGATCAGTCGTGG TAAAATGACCGAGGCCTGTG 2925–2948 0.857 74.3
rps16_p4 rps16 TAAGTGATAGGCCCCACCAA TAAAATGACCGAGGCCTGTG 2681–2704 0.857 74.3
rps16_p5 rps16 TTAAGTGATAGGCCCCACCA TAAAATGACCGAGGCCTGTG 2682–2705 0.857 74.3
rps16-trnS-GCU_p1 rps16-trnS-GCU AAGTCGCACGTTGCTTTCTA AGTACTAATTTCATCATGGGTCT 1086–1089 1.000 41.2
rps16-trnS-GCU_p2 rps16-trnS-GCU TGATGTCCTTCAAGTCGCAC AGTACTAATTTCATCATGGGTCT 1097–1100 1.000 41.2
rps16-trnS-GCU_p3 rps16-trnS-GCU AAGTCGCACGTTGCTTTCTA AGTACTAATTTCATCATGGGTC 1086–1089 1.000 41.2
rps16-trnS-GCU_p4 rps16-trnS-GCU AAGTCGCACGTTGCTTTCTA GTACTAATTTCATCATGGGTCT 1085–1088 1.000 41.2
rps16-trnS-GCU_p5 rps16-trnS-GCU TGATGTCCTTCAAGTCGCAC GTACTAATTTCATCATGGGTCT 1096–1099 1.000 41.2
trnS-GCU-psbI_p1 trnS-GCU-psbI CACAGGCCTCGGTCATTTTA GAGGTTCGAATCCTTCCGTC 1113–1147 1.000 82.5
trnS-GCU-psbI_p2 trnS-GCU-psbI CACAGGCCTCGGTCATTTTA CGTCCCAGGTTGATTCCAAT 1097–1131 1.000 82.1
trnS-GCU-psbI_p3 trnS-GCU-psbI AGCTTACCTTGCTTTGCTGA GAGGTTCGAATCCTTCCGTC 842–873 1.000 81.7
trnS-GCU-psbI_p4 trnS-GCU-psbI CACAGGCCTCGGTCATTTTA CTTCCGTCCCAGGTTGATTC 1101–1135 1.000 81.1
trnS-GCU-psbI_p5 trnS-GCU-psbI CGGATCCATTACACCCAACC GAGGTTCGAATCCTTCCGTC 1195–1229 1.000 80.5
trnQ-UUG-trnG-UCC_p1 trnQ-UUG-trnG-UCC TCTTGGAGGTTGTGTAATGCT ACGAATCACACTTTTACCACT 1228–1247 1.000 42.1
trnQ-UUG-trnG-UCC_p2 trnQ-UUG-trnG-UCC TCTTGGAGGTTGTGTAATGCT AGAACGAATCACACTTTTACCAC 1231–1250 1.000 42.1
trnQ-UUG-trnG-UCC_p3 trnQ-UUG-trnG-UCC TCTTGGAGGTTGTGTAATGCT GAACGAATCACACTTTTACCACT 1230–1249 1.000 42.1
trnQ-UUG-trnG-UCC_p4 trnQ-UUG-trnG-UCC TCTTGGAGGTTGTGTAATGCT AACGAATCACACTTTTACCACT 1229–1248 1.000 42.1
trnQ-UUG-trnG-UCC_p5 trnQ-UUG-trnG-UCC TCTTGGAGGTTGTGTAATGCTT ACGAATCACACTTTTACCACT 1228–1247 1.000 42.1
atpF-atpH_p1 atpF-atpH AATGGCCCAAGGAAACGAAA TTTACGGATTGGTCGTAGCA 664–674 1.000 70.2
atpF-atpH_p2 atpF-atpH AATGGCCCAAGGAAACGAAA TGGTCGTAGCATTAGCACTT 655–665 1.000 70.1
atpF-atpH_p3 atpF-atpH AATGGCCCAAGGAAACGAAA TTGGTCGTAGCATTAGCACT 656–666 1.000 70.1
atpF-atpH_p4 atpF-atpH AATGGCCCAAGGAAACGAAA ACGGATTGGTCGTAGCATTAG 661–671 1.000 69.8
atpF-atpH_p5 atpF-atpH AATGGCCCAAGGAAACGAAA GGATTGGTCGTAGCATTAGCA 659–669 1.000 69.2
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACCTTAGCCGC 1082–1085 1.000 79.7
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACCTTAGCCGC 1138–1141 1.000 79.1
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA ATTTTTGCAACCTTAGCCGC 1083–1086 1.000 78.6
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC ATTTTTGCAACCTTAGCCGC 1142–1145 1.000 78.5
atpH-atpI_p5 atpH-atpI TCCAGCAGCAATAACGGAAG ATTTTTGCAACCTTAGCCGC 1092–1095 1.000 77.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Alisma canaliculatum OR999289.1 159629 View on NCBI ↗
Alisma gramineum OR999291.1 159925 View on NCBI ↗
Alisma lanceolatum OR999292.1 159543 View on NCBI ↗
Alisma plantago-aquatica subsp. orientale OR999299.1 159853 View on NCBI ↗
Alisma subcordatum NC_085164.1 160180 View on NCBI ↗
Alisma triviale NC_085165.1 159727 View on NCBI ↗
Alisma wahlenbergii PV541173.1 159931 View on NCBI ↗