Markers + reference

Spathiphyllum

2 species · Araceae · Alismatales

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Species 2
Genome length 163–165 kb
Candidate markers 269
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 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 490 0.1462 0.95 89.1 yes View details
tRNA-Ser(GCU)-tRNA-Gly(UCC) LSC 1377 0.1501 0.67 77.8 yes View details
rps4-tRNA-Thr(UGU) LSC 448 0.1432 0.98 84.0 yes View details
tRNA-Thr(UGU)-tRNA-Leu(UAA) LSC 1177 0.0370 0.80 75.7 yes View details
clpP LSC 2084 0.0240 0.98 59.5 yes View details
tRNA-Asn(GUU)-ndhF SSC 1079 0.2207 0.68 78.9 yes View details
psaC-ndhE SSC 945 0.0749 0.79 75.4 yes View details
rps15-ycf1 SSC 969 0.1685 0.92 83.8 yes View details
ndhE-ndhG SSC 388 0.0503 0.82 83.2 yes View details
tRNA-Phe(GAA)-ndhJ LSC 835 0.0435 0.99 81.7 yes View details
tRNA-Leu(CAA)-ndhB IRb 773 0.0319 0.93 81.2 yes View details
ndhB-tRNA-Leu(CAA) IRa 773 0.0319 0.93 81.2 yes View details
psbT-psbN LSC 67 0.0746 1.00 80.5 yes View details
ccsA-ndhD SSC 238 0.0622 0.95 76.3 yes View details
petA-psbJ LSC 923 0.0275 0.98 76.1 yes View details
rpl22-rps19 LSC 108 0.1028 0.99 74.7 yes View details
tRNA-Asp(GUC) LSC 72 0.0417 1.00 74.1 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
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG CACGCCCAGGATTACGTC 623–625 1.000 73.9
psbK-psbI_p2 psbK-psbI ATGCCCGTCATACCTGTACT CACGCCCAGGATTACGTC 662–664 1.000 72.5
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCACGCCCAGGATTACGT 624–626 1.000 72.4
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT CACGCCCAGGATTACGTC 620–622 1.000 71.9
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT CACGCCCAGGATTACGTC 621–623 1.000 71.9
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p1 tRNA-Ser(GCU)-tRNA-Gly(UCC) GCTTTAGTCCACTCAGCCAT AGGACGAATCACACTTTTACCA 997–1440 1.000 70.0
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p2 tRNA-Ser(GCU)-tRNA-Gly(UCC) GCTTTAGTCCACTCAGCCAT GGACGAATCACACTTTTACCAC 996–1439 1.000 69.5
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p3 tRNA-Ser(GCU)-tRNA-Gly(UCC) AGTCCACTCAGCCATCTCTC AGGACGAATCACACTTTTACCA 992–1435 1.000 69.1
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p4 tRNA-Ser(GCU)-tRNA-Gly(UCC) AGTCCACTCAGCCATCTCTC GGACGAATCACACTTTTACCAC 991–1434 1.000 68.7
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p5 tRNA-Ser(GCU)-tRNA-Gly(UCC) TAGTCCACTCAGCCATCTCT AGGACGAATCACACTTTTACCA 993–1436 1.000 66.5
tRNA-Asp(GUC)_p1 tRNA-Asp(GUC) CCCAAGCAGTAGAAGTGCAA ATGTATGCTGTACATCCCGC 192–794 1.000 78.3
tRNA-Asp(GUC)_p2 tRNA-Asp(GUC) TGGCTATAGACCCAAGCAGT ATGTATGCTGTACATCCCGC 202–804 1.000 78.2
tRNA-Asp(GUC)_p3 tRNA-Asp(GUC) GACCCAAGCAGTAGAAGTGC ATGTATGCTGTACATCCCGC 194–796 1.000 74.7
tRNA-Asp(GUC)_p4 tRNA-Asp(GUC) CCCAAGCAGTAGAAGTGCAA TGTATGCTGTACATCCCGCT 191–793 1.000 72.6
tRNA-Asp(GUC)_p5 tRNA-Asp(GUC) TGGCTATAGACCCAAGCAGT TGTATGCTGTACATCCCGCT 201–803 1.000 72.5
rps4-tRNA-Thr(UGU)_p1 rps4-tRNA-Thr(UGU) AGAGCGCAGTTGGGTTTTAA GATGGTCATCGGTTCGACTC 594–885 1.000 86.2
rps4-tRNA-Thr(UGU)_p2 rps4-tRNA-Thr(UGU) AGCGCAGTTGGGTTTTAAGA GATGGTCATCGGTTCGACTC 592–883 1.000 86.2
rps4-tRNA-Thr(UGU)_p3 rps4-tRNA-Thr(UGU) AGAGCGCAGTTGGGTTTTAA CTCAGAGGTTAGAGCATCGC 625–916 1.000 86.1
rps4-tRNA-Thr(UGU)_p4 rps4-tRNA-Thr(UGU) AGCGCAGTTGGGTTTTAAGA CTCAGAGGTTAGAGCATCGC 623–914 1.000 86.1
rps4-tRNA-Thr(UGU)_p5 rps4-tRNA-Thr(UGU) GAGCGCAGTTGGGTTTTAAG CTCAGAGGTTAGAGCATCGC 624–915 1.000 83.7
tRNA-Thr(UGU)-tRNA-Leu(UAA)_p1 tRNA-Thr(UGU)-tRNA-Leu(UAA) GGAAAAAGCCAGCTATCGGA ACCAATTTCGCCATATCCCC 1097–1276 1.000 86.0
tRNA-Thr(UGU)-tRNA-Leu(UAA)_p2 tRNA-Thr(UGU)-tRNA-Leu(UAA) AGGGAAAAAGCCAGCTATCG ACCAATTTCGCCATATCCCC 1099–1278 1.000 86.0
tRNA-Thr(UGU)-tRNA-Leu(UAA)_p3 tRNA-Thr(UGU)-tRNA-Leu(UAA) GGAAAAAGCCAGCTATCGGA TCCATACCAAGGCTCAATGC 1136–1315 1.000 85.5
tRNA-Thr(UGU)-tRNA-Leu(UAA)_p4 tRNA-Thr(UGU)-tRNA-Leu(UAA) AGGGAAAAAGCCAGCTATCG TCCATACCAAGGCTCAATGC 1138–1317 1.000 85.5
tRNA-Thr(UGU)-tRNA-Leu(UAA)_p5 tRNA-Thr(UGU)-tRNA-Leu(UAA) GGAAAAAGCCAGCTATCGGA TAGCGTCTACCAATTTCGCC 1105–1284 1.000 85.5
tRNA-Phe(GAA)-ndhJ_p1 tRNA-Phe(GAA)-ndhJ CCTCGTGTCACCAGTTCAAA TGAAAGTTGGATAGGCTGGC 945–1201 1.000 81.8
tRNA-Phe(GAA)-ndhJ_p2 tRNA-Phe(GAA)-ndhJ AGTGATGCATGGAAAACGGT TGAAAGTTGGATAGGCTGGC 1002–1258 1.000 81.4
tRNA-Phe(GAA)-ndhJ_p3 tRNA-Phe(GAA)-ndhJ GTGATGCATGGAAAACGGTC TGAAAGTTGGATAGGCTGGC 1001–1257 1.000 80.0
tRNA-Phe(GAA)-ndhJ_p4 tRNA-Phe(GAA)-ndhJ CATGGAAAACGGTCGGGATA TGAAAGTTGGATAGGCTGGC 995–1251 1.000 79.6
tRNA-Phe(GAA)-ndhJ_p5 tRNA-Phe(GAA)-ndhJ CCTCGTGTCACCAGTTCAAA ATCATCCACGCCTTAAACGT 976–1232 1.000 79.6

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
Spathiphyllum kochii NC_030371.1 163368 View on NCBI ↗
Spathiphyllum patulinervum NC_047233.1 164751 View on NCBI ↗