Markers + reference

Aloe

3 species · Asphodelaceae · Asparagales

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Species 3
Genome length 152–153 kb
Candidate markers 261
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 661 0.0265 0.99 66.7 yes View details
rps16-trnQ-UUG LSC 1071 0.0206 1.00 62.8 yes View details
trnS-GCU-trnG-UCC LSC 485 0.0266 0.98 62.3 yes View details
trnE-UUC-trnT-GGU LSC 295 0.0295 1.00 64.6 yes View details
trnT-GGU-psbD LSC 984 0.0149 1.00 59.5 yes View details
ndhC-trnV-UAC LSC 709 0.0217 1.00 64.1 yes View details
petA-psbJ LSC 1128 0.0297 1.00 67.9 yes View details
petD LSC 1228 0.0090 1.00 51.2 yes View details
infA LSC 183 0.0255 1.00 55.4 yes View details
ycf1 IRb 1239 0.0070 0.99 48.9 no View details
ndhF SSC 2220 0.0108 1.00 51.2 yes View details
ycf1 SSC 5400 0.0133 0.99 48.3 yes View details
petD-rpoA LSC 195 0.0547 1.00 71.1 yes View details
rps11-rpl36 LSC 129 0.0312 0.99 70.1 yes View details
psaC-ndhE SSC 361 0.0240 1.00 69.1 yes View details
rps19-psbA LSC 131 0.0484 0.89 68.3 no View details
psbK-psbI LSC 414 0.0220 0.99 66.2 yes View details
rpl20-clpP1 LSC 997 0.0127 1.00 62.9 yes View details
trnR-ACG-trnN-GUU IRb 596 0.0056 1.00 62.2 yes View details
trnN-GUU-trnR-ACG IRa 596 0.0056 1.00 62.2 yes View details
rps15-ycf1 SSC 349 0.0253 0.98 61.3 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGAGGAAGGCAGAATTATTGA 736–739 1.000 47.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGAGGAAGGCAGAATTATTGA 735–738 1.000 47.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGAGGAAGGCAGAATTATTGAA 736–739 1.000 46.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGAGGAAGGCAGAATTATTGAA 735–738 1.000 46.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTGAGGAAGGCAGAATTATTGA 736–739 1.000 46.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1151–1169 1.000 82.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GTCACTCGGAGGTTCGAATC 1159–1177 1.000 82.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 1153–1171 1.000 81.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1144–1162 1.000 81.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG CTCGGAGGTTCGAATCCTTC 1155–1173 1.000 81.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGCCCGGATCGTTAGATAAG 498–532 1.000 82.5
psbK-psbI_p2 psbK-psbI ATGCCCGTCATACCTGTACT GGCCCGGATCGTTAGATAAG 537–571 1.000 81.1
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGCCCGGATCGTTAGATAAG 495–529 1.000 80.5
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT GGCCCGGATCGTTAGATAAG 496–530 1.000 80.5
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT GGCCCGGATCGTTAGATAAG 497–531 1.000 80.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AGATTAGCAATCTGCCGCTT GGGAAAAAGGACGAAACCCT 647–663 1.000 81.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA GGGAAAAAGGACGAAACCCT 693–709 1.000 81.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TTCCTCGTTCTGACCTTCCA GGGAAAAAGGACGAAACCCT 1169–1189 1.000 80.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TTCCTCGTTCTGACCTTCCA CATCGTTAGCTTGGAAGGCT 1769–1792 1.000 80.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TTCCTCGTTCTGACCTTCCA CGTTAGCTTGGAAGGCTAGG 1766–1789 1.000 80.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 375–390 1.000 81.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 396–411 1.000 81.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 354–369 1.000 81.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 375–390 1.000 81.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 372–387 1.000 81.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCCTCCGTAACCAATCATCC 1118–1122 1.000 79.0
trnT-GGU-psbD_p2 trnT-GGU-psbD TGAATTGAATAGGGCAGGGC CCCTCCGTAACCAATCATCC 1150–1154 1.000 78.9
trnT-GGU-psbD_p3 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CCCTCCGTAACCAATCATCC 1121–1125 1.000 78.8
trnT-GGU-psbD_p4 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA CCCTCCGTAACCAATCATCC 1095–1099 1.000 77.3
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCCCTTTTAACTCAGTGGT CCCTCCGTAACCAATCATCC 1133–1137 1.000 77.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Aloe arborescens NC_066013.1 152364 View on NCBI ↗
Aloe maculata NC_035505.1 153175 View on NCBI ↗
Aloe vera NC_035506.1 152875 View on NCBI ↗