Markers + reference

Hippeastrum

9 species · Amaryllidaceae · Asparagales

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Species 9
Genome length 158–159 kb
Candidate markers 272
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0007 1.00 29.9 yes View details
atpF-atpH LSC 495 0.0059 1.00 41.8 yes View details
rbcL-accD LSC 798 0.0042 1.00 51.4 yes View details
petA-psbJ LSC 1157 0.0063 1.00 49.2 yes View details
ycf1 IRb 981 0.0008 1.00 28.4 no View details
ndhD SSC 1506 0.0019 1.00 36.7 yes View details
ycf1 SSC 5442 0.0037 1.00 44.2 yes View details
rps19-psbA LSC 137 0.0211 1.00 61.6 no View details
trnT-UGU-trnL-UAA LSC 1010 0.0013 1.00 57.7 yes View details
psaJ-rpl33 LSC 488 0.0023 1.00 51.9 yes View details
petN-psbM LSC 987 0.0022 1.00 51.1 yes View details
psbB-psbT LSC 190 0.0076 0.99 51.0 yes View details
rpl20-rps12 LSC 741 0.0027 1.00 48.6 yes View details
psbM-trnD-GUC LSC 1040 0.0012 1.00 47.6 yes View details
rpoB LSC 3213 0.0011 1.00 47.5 yes View details
rpl2 IRb 1491 0.0008 1.00 46.9 yes View details
rpl2 IRa 1491 0.0008 1.00 46.9 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TGGGTATGGCTCCTTAAACG TTGCGAAGATTAGGTTCGGG 1812–1814 0.889 70.2
psbA_p2 psbA TGGGTATGGCTCCTTAAACG GTGCTTGGGAGTCCTTGAAA 1151 0.889 69.9
psbA_p3 psbA TGGGTATGGCTCCTTAAACG CATAGGGAAAGTCGTGTGCA 1475 0.889 69.6
psbA_p4 psbA TGGGTATGGCTCCTTAAACG ACATAGGGAAAGTCGTGTGC 1476 0.889 69.6
psbA_p5 psbA TGGGTATGGCTCCTTAAACG GTTTGGGGAGGGGTCTTTTT 1437 0.889 69.5
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG GTCGTGGCATTAGCACTTTT 604–607 1.000 72.6
atpF-atpH_p2 atpF-atpH CAGTGGCCTAAGGAAACGAA GTCGTGGCATTAGCACTTTT 576–579 1.000 72.2
atpF-atpH_p3 atpF-atpH AGTGGCCTAAGGAAACGAAA GTCGTGGCATTAGCACTTTT 575–578 1.000 66.1
atpF-atpH_p4 atpF-atpH CCAGTGGCCTAAGGAAACG GTCGTGGCATTAGCACTTTT 577–580 1.000 64.4
atpF-atpH_p5 atpF-atpH AGTGGCCTAAGGAAACGAAAG GTCGTGGCATTAGCACTTTT 575–578 1.000 63.8
rpoB_p1 rpoB CCGCGGGGACATATAATTCA TCCGGAATGGAAATGAGGGA 249 1.000 73.6
rpoB_p2 rpoB CCGCGGGGACATATAATTCA CCGGAATGGAAATGAGGGAA 248 1.000 73.4
rpoB_p3 rpoB TTCCAAATTAATCCCGCGGG TCCGGAATGGAAATGAGGGA 262 1.000 72.5
rpoB_p4 rpoB TTCCAAATTAATCCCGCGGG CCGGAATGGAAATGAGGGAA 261 1.000 72.3
rpoB_p5 rpoB TCCCGCGGGGACATATAATT TCCGGAATGGAAATGAGGGA 251 1.000 72.2
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 1123–1145 1.000 70.9
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 1072–1094 1.000 70.1
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 1071–1093 1.000 70.1
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTGTTCATTCT 1070–1092 1.000 69.6
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 1129–1151 1.000 69.4
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC AGTTCAATCGGTCAGAGCAC 1151–1154 1.000 62.0
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TACACCTCACCGGGATTGTA 1170–1173 1.000 60.8
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CCTCACCGGGATTGTAGTTC 1166–1169 1.000 60.2
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC ACCTCACCGGGATTGTAGTT 1167–1170 1.000 59.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC ATACACCTCACCGGGATTGT 1171–1174 1.000 59.3
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1035–1090 1.000 83.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1043–1098 1.000 82.8
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1067–1122 1.000 82.5
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG GGAAGTTCCCACTTAGCAGG 1096–1151 1.000 82.4
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1075–1130 1.000 82.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Hippeastrum alberti NC_059686.1 158067 View on NCBI ↗
Hippeastrum aulicum PX696961.1 158101 View on NCBI ↗
Hippeastrum curitibanum PX724629.1 158113 View on NCBI ↗
Hippeastrum haywardii PX724626.1 158081 View on NCBI ↗
Hippeastrum hybrid cultivar NC_059685.1 158067 View on NCBI ↗
Hippeastrum nelsonii PX724627.1 158357 View on NCBI ↗
Hippeastrum psittacinum PX724631.1 158116 View on NCBI ↗
Hippeastrum reticulatum NC_059687.1 158522 View on NCBI ↗
Hippeastrum vittatum NC_052724.1 158082 View on NCBI ↗