Markers + reference

Sida

4 species · Malvaceae · Malvales

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Species 4
Genome length 160–160 kb
Candidate markers 266
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 395 0.0575 0.83 80.5 yes View details
trnK-UUU-rps16 LSC 870 0.0106 0.97 56.5 yes View details
trnT-GGU-psbD LSC 1489 0.0145 0.99 62.8 yes View details
psbZ-trnG-GCC LSC 738 0.0210 0.96 68.1 yes View details
rps4-trnT-UGU LSC 504 0.0201 0.95 74.8 yes View details
psbE-petL LSC 893 0.0122 0.99 67.8 yes View details
clpP LSC 2146 0.0066 0.99 49.2 yes View details
petD LSC 1240 0.0028 1.00 40.6 yes View details
rpl16 LSC 1562 0.0041 0.98 49.8 yes View details
ndhF SSC 2208 0.0051 1.00 48.9 yes View details
ccsA-ndhD SSC 301 0.0296 0.95 53.1 yes View details
ycf1 IRb 81 0.1692 0.80 75.2 yes View details
psaA-ycf3 LSC 988 0.0070 0.99 67.2 yes View details
petD-rpoA LSC 237 0.0380 1.00 65.7 yes View details
cemA-petA LSC 237 0.0115 0.98 65.5 yes View details
rpl2-trnH-GUG IRa 148 0.0333 0.89 64.6 no View details
trnS-GCU-trnG-GCC LSC 797 0.0121 0.98 64.3 yes View details
rpl32-trnL-UAG SSC 1184 0.0068 0.94 63.9 yes View details
psaJ-rpl33 LSC 518 0.0134 0.96 63.1 yes View details
ndhF-rpl32 SSC 898 0.0069 0.99 62.1 yes View details
petN-psbM LSC 1097 0.0037 0.99 61.9 yes View details
ycf1 SSC 5694 0.0062 0.99 44.1 no 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 TTCCCTCTAGACCTAGCTGC 390–465 1.000 88.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 404–479 1.000 88.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 403–478 1.000 88.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 405–480 1.000 88.4
trnH-GUG-psbA_p5 trnH-GUG-psbA AAAAATGACATGGGCGAACG TTCCCTCTAGACCTAGCTGC 530 0.250 46.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1232–1273 1.000 83.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 1233–1274 1.000 83.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1293–1334 1.000 82.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GAGAAAAAGGGGCATGTTGC 1718–1758 1.000 82.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CCCAATGAGCCGTTTATCGA 1228–1269 1.000 82.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAATCAAACCGAGAGACCCC 891–910 1.000 83.5
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAATCAAACCGAGAGACCCC 890–909 1.000 83.5
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CGCACAACGGATTAGCAATC GAATCAAACCGAGAGACCCC 906–925 1.000 82.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CCGAGAGACCCCTTAACTCT 883–902 1.000 82.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CCGAGAGACCCCTTAACTCT 882–901 1.000 82.6
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA ATTGCTACAGCGCTGTTCAT 1254–1291 1.000 78.9
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA TATTGCTACAGCGCTGTTCA 1255–1292 1.000 77.9
petN-psbM_p3 petN-psbM AGTAAGTCTTGCTTGGGCTG ATTGCTACAGCGCTGTTCAT 1260–1297 1.000 77.4
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TTGCTACAGCGCTGTTCATT 1253–1290 1.000 77.1
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TATTGCTACAGCGCTGTTCA 1261–1298 1.000 76.4
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG AAAAACGAACCGGTCCCTAC 1637–1681 1.000 81.4
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CAAAAACGAACCGGTCCCTA 1638–1682 1.000 81.4
trnT-GGU-psbD_p3 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA AAAAACGAACCGGTCCCTAC 1640–1684 1.000 81.3
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CAAAAACGAACCGGTCCCTA 1641–1685 1.000 81.3
trnT-GGU-psbD_p5 trnT-GGU-psbD ACGGCCCTTTTAACTCAGTG AAAAACGAACCGGTCCCTAC 1654–1698 1.000 81.1
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 883–930 1.000 83.2
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTT CGTCTTCTCCTTGGCAAAGA 881–928 1.000 83.2
psbZ-trnG-GCC_p3 psbZ-trnG-GCC CTCCTGATGGTTGGTTGAGT CGTCTTCTCCTTGGCAAAGA 877–924 1.000 77.9
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TGCTTCTCCTGATGGTTGGT CGTCTTCTCCTTGGCAAAGA 882–929 1.000 77.4
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TCTCCTGATGGTTGGTTGAG CGTCTTCTCCTTGGCAAAGA 878–925 1.000 75.6

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
Sida cuspidata OR162023.1 160117 View on NCBI ↗
Sida fallax NC_080995.1 160058 View on NCBI ↗
Sida rhombifolia OR162024.1 159852 View on NCBI ↗
Sida szechuensis NC_051877.1 159878 View on NCBI ↗