Markers + reference

Sparganium

17 species · Typhaceae · Poales

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Species 17
Genome length 162–162 kb
Candidate markers 274
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 1599 0.0269 0.98 71.5 yes View details
atpH-atpI LSC 949 0.0211 0.99 65.9 yes View details
trnT-UGU-trnL-UAA LSC 1084 0.0166 0.99 68.1 yes View details
accD-psaI LSC 1224 0.0234 0.99 69.1 yes View details
petA-psbJ LSC 1143 0.0198 1.00 58.7 yes View details
ycf1 IRb 1179 0.0145 0.99 58.0 yes View details
ndhF-rpl32 SSC 954 0.0269 0.99 73.8 yes View details
psaC-ndhE SSC 797 0.0321 0.99 71.5 yes View details
ycf1 SSC 5565 0.0123 1.00 48.3 no View details
petN-psbM LSC 1247 0.0126 0.99 67.6 yes View details
trnE-UUC-trnT-GGU LSC 765 0.0164 1.00 64.9 yes View details
rpoA-rps11 LSC 68 0.0222 1.00 63.8 yes View details
rps16-trnQ-UUG LSC 1152 0.0126 1.00 63.6 yes View details
psbK-psbI LSC 433 0.0197 0.98 63.5 yes View details
ycf1-ndhF SSC 135 0.1042 0.73 63.1 yes View details
trnW-CCA-trnP-UGG LSC 151 0.0261 1.00 60.9 yes View details
atpB-rbcL LSC 817 0.0092 1.00 60.5 yes View details
petD-rpoA LSC 215 0.0300 0.95 60.5 yes View details
rps19-psbA IRa 197 0.0253 0.98 60.0 no 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-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1222–1250 1.000 83.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1233–1261 1.000 82.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1226–1254 1.000 82.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1237–1265 1.000 81.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1228–1256 1.000 80.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACAAAGAGTTTGAGAGTAAGCA 471–492 1.000 53.3
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACAAAGAGTTTGAGAGTAAGCA 468–489 1.000 51.4
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACAAAGAGTTTGAGAGTAAGCA 469–490 1.000 51.4
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACAAAGAGTTTGAGAGTAAGCA 470–491 1.000 51.3
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACAAAGAGTTTGAGAGTAAGCA 472–493 1.000 51.1
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GGCGTTAATAGAACGAATCACA 1497–1802 1.000 66.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GGCGTTAATAGAACGAATCACAC 1497–1802 1.000 65.5
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AGGCGTTAATAGAACGAATCACA 1498–1803 1.000 64.9
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AGGCGTTAATAGAACGAATCAC 1498–1803 1.000 63.9
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GCTTTAGTCCACTCAGCCAT GGCGTTAATAGAACGAATCACA 1483–1788 1.000 63.1
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA CGAATCCATGGAGGGTCATC 983–1011 1.000 86.8
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA CGAATCCATGGAGGGTCATC 1001–1029 1.000 86.3
atpH-atpI_p3 atpH-atpI CAGCAGCAATAACAGAAGCG CGAATCCATGGAGGGTCATC 993–1021 1.000 86.2
atpH-atpI_p4 atpH-atpI GCCAATCCAGCAGCAATAAC CGAATCCATGGAGGGTCATC 1000–1028 1.000 85.8
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCT CGAATCCATGGAGGGTCATC 1023–1051 1.000 83.9
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1395–1411 1.000 72.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 1395–1411 1.000 68.1
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTCT 1396–1412 1.000 66.4
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTCT 1387–1403 1.000 66.3
petN-psbM_p5 petN-psbM TAGTATGGGGAAGGAGTGGG TGCTACTGCACTGTTCATTCT 1344–1354 0.941 66.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG GAACCGATGACTTACGCCTT 903–945 1.000 85.0
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG CCATGGCGTTACTCTACCAC 882–924 1.000 84.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG TGGCGTTACTCTACCACTGA 879–921 1.000 84.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG CCGATGACTTACGCCTTACC 900–942 1.000 83.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 868–910 1.000 83.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Sparganium acaule MW829767.1 161820 View on NCBI ↗
Sparganium angustifolium NC_058795.1 161720 View on NCBI ↗
Sparganium confertum NC_061351.1 161997 View on NCBI ↗
Sparganium emersum NC_061197.1 161760 View on NCBI ↗
Sparganium erectum NC_061198.1 161860 View on NCBI ↗
Sparganium erectum subsp. neglectum NC_061201.1 161810 View on NCBI ↗
Sparganium eurycarpum NC_058576.1 161812 View on NCBI ↗
Sparganium eurycarpum subsp. coreanum MK182317.1 161761 View on NCBI ↗
Sparganium fallax MW874418.1 161838 View on NCBI ↗
Sparganium fluctuans NC_061202.1 162191 View on NCBI ↗
Sparganium gramineum NC_061203.1 162053 View on NCBI ↗
Sparganium hyperboreum NC_061199.1 162331 View on NCBI ↗
Sparganium japonicum MW829762.1 161968 View on NCBI ↗
Sparganium natans NC_058577.1 161635 View on NCBI ↗
Sparganium stoloniferum NC_044634.1 161759 View on NCBI ↗
Sparganium stoloniferum subsp. choui MW829765.1 161865 View on NCBI ↗
Sparganium subglobosum NC_061352.1 161593 View on NCBI ↗