Markers + reference

Adromischus

4 species · Crassulaceae · Saxifragales

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Species 4
Genome length 150–151 kb
Candidate markers 261
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 310 0.0306 1.00 64.1 yes View details
rps16 LSC 1064 0.0088 1.00 55.5 yes View details
rps16-trnQ-UUG LSC 1497 0.0185 1.00 63.9 yes View details
rpoB-trnC-GCA LSC 1134 0.0159 0.99 63.8 yes View details
psbM-trnD-GUC LSC 970 0.0112 0.99 59.5 yes View details
psbZ-trnG-GCC LSC 604 0.0254 0.99 66.5 yes View details
petA-psbJ LSC 867 0.0258 1.00 77.6 yes View details
rps3 LSC 657 0.0023 1.00 38.1 yes View details
ccsA-ndhD SSC 245 0.0354 0.99 64.2 yes View details
ycf1 SSC 5082 0.0104 1.00 45.5 yes View details
rps3-rpl22 LSC 131 0.0878 0.95 77.8 yes View details
psbE-petL LSC 1163 0.0085 0.99 66.6 yes View details
trnS-GCU-trnG-GCC LSC 523 0.0147 0.93 65.5 yes View details
rbcL-accD LSC 595 0.0101 1.00 65.3 yes View details
psaI-cemA LSC 1400 0.0063 1.00 64.5 yes View details
petG-trnW-CCA LSC 119 0.0224 1.00 64.4 yes View details
trnK-UUU-rps16 LSC 721 0.0090 1.00 63.4 yes View details
psbA-trnK-UUU LSC 242 0.0172 1.00 63.3 yes View details
rps11-rpl36 LSC 118 0.0268 1.00 63.1 yes View details
trnP-UGG-psaJ LSC 349 0.0100 1.00 62.4 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 376–507 1.000 83.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 379–510 1.000 83.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 390–521 1.000 82.9
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 389–520 1.000 82.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 391–522 1.000 82.9
psbA-trnK-UUU_p1 psbA-trnK-UUU ATAGGCTTTCAGTTTCGCGT GGCTTGGGGAGAGTCTTTTT 375–388 1.000 78.6
psbA-trnK-UUU_p2 psbA-trnK-UUU AAACGACCCCATAGGCTTTC GGCTTGGGGAGAGTCTTTTT 385–398 1.000 78.3
psbA-trnK-UUU_p3 psbA-trnK-UUU CAAAAACGACCCCATAGGCT GGCTTGGGGAGAGTCTTTTT 388–401 1.000 78.0
psbA-trnK-UUU_p4 psbA-trnK-UUU ATAGGCTTTCAGTTTCGCGT AAAATGCAAACACGGCTTGG 388–401 1.000 77.5
psbA-trnK-UUU_p5 psbA-trnK-UUU AAACGACCCCATAGGCTTTC AAAATGCAAACACGGCTTGG 398–411 1.000 77.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA GTGCTAAACCGACAGGAACT 895–898 1.000 80.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC GTGCTAAACCGACAGGAACT 896–899 1.000 80.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC GTGCTAAACCGACAGGAACT 900–903 1.000 80.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT GTGCTAAACCGACAGGAACT 898–901 1.000 80.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC GTGCTAAACCGACAGGAACT 907–910 1.000 79.9
rps16_p1 rps16 ATCCGAGTCATACCCACACT TGACTACTCATGATTCCATTTCT 1116–1129 1.000 43.1
rps16_p2 rps16 AGATCCGAGTCATACCCACA TGACTACTCATGATTCCATTTCT 1118–1131 1.000 43.1
rps16_p3 rps16 ATCCGAGTCATACCCACACT ACCAAACTAATGACTACTCATGA 1126–1139 1.000 43.0
rps16_p4 rps16 ATCCGAGTCATACCCACACT CCAAACTAATGACTACTCATGATTCC 1125–1138 1.000 43.0
rps16_p5 rps16 AGATCCGAGTCATACCCACA ACCAAACTAATGACTACTCATGA 1128–1141 1.000 43.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1130–1576 1.000 84.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1141–1587 1.000 84.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTATGCGGAGGTTCGAATCC 1137–1583 1.000 83.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTATGCGGAGGTTCGAATCC 1148–1594 1.000 83.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 1153–1599 1.000 82.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACTATTAGG 608–711 1.000 60.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACTATTAGG 607–710 1.000 60.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA CGAAGGACCCCTTAACTATTAGG 626–729 1.000 59.4
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA CGAAGGACCCCTTAACTATTAGG 662–765 1.000 58.7
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GAATCGCTCGTACAACGGAT CGAAGGACCCCTTAACTATTAGG 631–734 1.000 58.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Adromischus cooperi PQ139281.1 150459 View on NCBI ↗
Adromischus cristatus var. schonlandii PQ139282.1 150960 View on NCBI ↗
Adromischus marianae PQ139284.1 150260 View on NCBI ↗
Adromischus triflorus PQ139285.1 150028 View on NCBI ↗