Markers + reference

Epipremnum

2 species · Araceae · Alismatales

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Species 2
Genome length 163–165 kb
Candidate markers 268
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNA-Glu(UUC)-tRNA-Thr(GGU) LSC 1031 0.1757 0.70 78.8 yes View details
ndhC-tRNA-Val(UAC) LSC 1141 0.2123 0.71 78.0 yes View details
accD LSC 1473 0.2356 0.83 81.3 yes View details
clpP LSC 2107 0.3467 0.54 72.2 yes View details
psaC-ndhE SSC 983 0.2050 0.89 84.3 yes View details
ycf1 SSC 5595 0.2066 0.95 77.1 yes View details
tRNA-Cys(GCA)-petN LSC 967 0.0940 0.90 86.3 yes View details
psbE-petL LSC 1179 0.1598 0.92 85.3 yes View details
tRNA-Ser(GCU)-tRNA-Ser (CGA) LSC 879 0.2195 0.96 84.6 yes View details
tRNA-Asn(GUU)-ndhF IRb 667 0.2057 0.95 84.4 yes View details
tRNA-Leu(CAA)-ndhB IRb 983 0.1113 0.79 84.0 yes View details
ndhB-tRNA-Leu(CAA) IRa 983 0.1113 0.79 84.0 yes View details
atpB-rbcL LSC 797 0.1501 0.91 83.1 yes View details
tRNA-Lys(UUU)-rps16 LSC 667 0.1006 0.92 82.8 yes View details
ycf3-tRNA-Ser(GGA) LSC 879 0.1166 0.97 82.8 yes View details
accD-psaI LSC 1069 0.1830 0.90 82.8 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
tRNA-Lys(UUU)-rps16_p1 tRNA-Lys(UUU)-rps16 CCTTTCAGGATCAGTCGTGG AAAGGAGCTCAACCCACAAG 860–950 1.000 89.7
tRNA-Lys(UUU)-rps16_p2 tRNA-Lys(UUU)-rps16 CCTTTCAGGATCAGTCGTGG AGCTCAACCCACAAGAACTG 855–945 1.000 89.6
tRNA-Lys(UUU)-rps16_p3 tRNA-Lys(UUU)-rps16 TAAGAACAGAAGCTCGTCGC AAAGGAGCTCAACCCACAAG 1069–1169 1.000 89.2
tRNA-Lys(UUU)-rps16_p4 tRNA-Lys(UUU)-rps16 TAAGAACAGAAGCTCGTCGC AGCTCAACCCACAAGAACTG 1064–1164 1.000 89.2
tRNA-Lys(UUU)-rps16_p5 tRNA-Lys(UUU)-rps16 CCTTTCAGGATCAGTCGTGG AGAGATCTTCGGAGAGTGGG 944–1034 1.000 89.1
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p1 tRNA-Ser(GCU)-tRNA-Ser (CGA) AGTCCACTCAGCCATCTCTC AGGACGAATCACACTTTTACCA 937–1629 1.000 67.4
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p2 tRNA-Ser(GCU)-tRNA-Ser (CGA) AGTCCACTCAGCCATCTCTC GGACGAATCACACTTTTACCAC 936–1628 1.000 66.9
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p3 tRNA-Ser(GCU)-tRNA-Ser (CGA) TAGTCCACTCAGCCATCTCT AGGACGAATCACACTTTTACCA 938–1630 1.000 64.8
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p4 tRNA-Ser(GCU)-tRNA-Ser (CGA) TAGTCCACTCAGCCATCTCT GGACGAATCACACTTTTACCAC 937–1629 1.000 64.4
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p5 tRNA-Ser(GCU)-tRNA-Ser (CGA) AGTCCACTCAGCCATCTCTC GGACGAATCACACTTTTACCA 936–1628 1.000 63.7
tRNA-Cys(GCA)-petN_p1 tRNA-Cys(GCA)-petN AGTTCAAATCTGGGTGTCGC CTCCTCCCCCATACTACGAG 1021–1069 1.000 85.8
tRNA-Cys(GCA)-petN_p2 tRNA-Cys(GCA)-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 968–1016 1.000 85.6
tRNA-Cys(GCA)-petN_p3 tRNA-Cys(GCA)-petN GGGGGACTGCAAATCCTTTA CTCCTCCCCCATACTACGAG 1046–1094 1.000 85.2
tRNA-Cys(GCA)-petN_p4 tRNA-Cys(GCA)-petN GGGGGACTGCAAATCCTTTA AGCCCAAGCGAGACTTACTA 993–1041 1.000 85.0
tRNA-Cys(GCA)-petN_p5 tRNA-Cys(GCA)-petN AGTTCAAATCTGGGTGTCGC TCTAAAGTCCACTCCTCCCC 1032–1080 1.000 84.4
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p1 tRNA-Glu(UUC)-tRNA-Thr(GGU) AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 785–1095 1.000 90.3
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p2 tRNA-Glu(UUC)-tRNA-Thr(GGU) AGATGTCCTGAACCGCTAGA TGGCGTTACTCTACCACTGA 782–1092 1.000 90.1
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p3 tRNA-Glu(UUC)-tRNA-Thr(GGU) GATGTCCTGAACCGCTAGAC CCATGGCGTTACTCTACCAC 784–1094 1.000 89.8
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p4 tRNA-Glu(UUC)-tRNA-Thr(GGU) GATGTCCTGAACCGCTAGAC TGGCGTTACTCTACCACTGA 781–1091 1.000 89.6
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p5 tRNA-Glu(UUC)-tRNA-Thr(GGU) GAGATGTCCTGAACCGCTAG CCATGGCGTTACTCTACCAC 786–1096 1.000 87.5
ycf3-tRNA-Ser(GGA)_p1 ycf3-tRNA-Ser(GGA) ACACGACAGAAGGCATTGTT CCCTCGGTAAACAAAAGCCT 1236–1253 1.000 89.8
ycf3-tRNA-Ser(GGA)_p2 ycf3-tRNA-Ser(GGA) GTCATCCTTCCTGCAAGAGG CCCTCGGTAAACAAAAGCCT 1643–1656 1.000 88.1
ycf3-tRNA-Ser(GGA)_p3 ycf3-tRNA-Ser(GGA) TTTCTTTGTCCCTAACGCCC CCCTCGGTAAACAAAAGCCT 1568–1589 1.000 87.4
ycf3-tRNA-Ser(GGA)_p4 ycf3-tRNA-Ser(GGA) ACACGACAGAAGGCATTGTT GGACAATTTTGCCCGCTTTT 1558 0.500 58.8
ycf3-tRNA-Ser(GGA)_p5 ycf3-tRNA-Ser(GGA) GTCATCCTTCCTGCAAGAGG GGACAATTTTGCCCGCTTTT 1965 0.500 58.7
ndhC-tRNA-Val(UAC)_p1 ndhC-tRNA-Val(UAC) AGAGAAGCGGCCATAAACTG GAGCAAATGGAGCCATCTCA 1582–1881 1.000 91.4
ndhC-tRNA-Val(UAC)_p2 ndhC-tRNA-Val(UAC) AGAGAAGCGGCCATAAACTG TCAGAGCAAATGGAGCCATC 1585–1884 1.000 91.4
ndhC-tRNA-Val(UAC)_p3 ndhC-tRNA-Val(UAC) AGAGAAGCGGCCATAAACTG CAGAGCAAATGGAGCCATCT 1584–1883 1.000 91.3
ndhC-tRNA-Val(UAC)_p4 ndhC-tRNA-Val(UAC) ACTAGAGAGCTTCTCCGGTC GAGCAAATGGAGCCATCTCA 1177–1473 1.000 91.2
ndhC-tRNA-Val(UAC)_p5 ndhC-tRNA-Val(UAC) ACTAGAGAGCTTCTCCGGTC TCAGAGCAAATGGAGCCATC 1180–1476 1.000 91.2

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
Epipremnum amplissimum NC_047232.1 163335 View on NCBI ↗
Epipremnum aureum NC_027954.2 164831 View on NCBI ↗