Markers + reference

Pterospermum

3 species · Malvaceae · Malvales

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Species 3
Genome length 163–163 kb
Candidate markers 265
Primer pairs 80

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 11 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU LSC 557 0.0545 0.92 77.1 yes View details
atpF-atpH LSC 662 0.0187 0.97 71.5 yes View details
rps4-trnT-UGU LSC 745 0.0448 0.98 69.2 yes View details
rpl33-rps18 LSC 583 0.0280 0.90 66.1 yes View details
trnN-GUU-ndhF IRb 547 0.0243 0.95 50.0 yes View details
ndhF-rpl32 SSC 1279 0.1616 0.88 83.4 yes View details
ycf1 SSC 5778 0.0122 1.00 33.5 yes View details
trnL-CAA-ndhB IRb 633 0.0021 0.99 60.7 yes View details
rpl22-rps19 LSC 257 0.0419 0.68 60.2 yes View details
rpl2-trnH-GUG IRa 80 0.0164 0.76 58.5 no View details
ndhC-trnM-CAU LSC 1978 0.0070 0.99 57.6 yes View details
trnK-UUU-rps16 LSC 941 0.0061 0.93 54.1 yes View details
trnT-UGU-trnL-UAA LSC 1075 0.0040 0.94 53.0 yes View details
rps16-trnQ-UUG LSC 570 0.0183 0.96 52.4 yes View details
atpB-rbcL LSC 1002 0.0115 0.99 52.3 yes View details
psaJ-rpl33 LSC 522 0.0053 0.96 52.0 yes View details
rpl2 IRa 1517 0.0022 1.00 51.3 yes View details
rpl2 IRb 1517 0.0004 1.00 46.9 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU AACACCAAACCATCCGATGT CGGTTTGGGGAGGGATTTTT 768–769 1.000 83.2
psbA-trnK-UUU_p2 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA CGGTTTGGGGAGGGATTTTT 744–745 1.000 82.9
psbA-trnK-UUU_p3 psbA-trnK-UUU AACACCAAACCATCCGATGT AAAATGCAAGCACGGTTTGG 780–781 1.000 82.7
psbA-trnK-UUU_p4 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA AAAATGCAAGCACGGTTTGG 756–757 1.000 82.4
psbA-trnK-UUU_p5 psbA-trnK-UUU AACACCAAACCATCCGATGT ACTCCATCCGACTAGTTCCG 704–705 1.000 81.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAGGAGCTCAACCCACAG 1032–1069 1.000 83.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGAGCTCAACCCACAG 1031–1068 1.000 83.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC AAAAGGAGCTCAACCCACAG 1018–1055 1.000 80.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGAAGGCGGGGGTTTTTAC 992–1029 1.000 80.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGAAGGCGGGGGTTTTTAC 991–1028 1.000 80.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AGTGGTGGGTTTTGACATCC GAGGTTCGAATCCTTCCGTC 686–780 1.000 83.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 643–737 1.000 82.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 654–748 1.000 82.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTTTGACATCCACAGCCGAT GAGGTTCGAATCCTTCCGTC 677–771 1.000 82.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTTGACATCCACAGCCGATC GAGGTTCGAATCCTTCCGTC 676–770 1.000 81.5
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA TGGTTGTAGCATTGGCACTT 747–785 1.000 83.8
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TGGTTGTAGCATTGGCACTT 775–813 1.000 83.0
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA CTGGTTGTAGCATTGGCACT 748–786 1.000 80.1
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA ATGGGCTGGTTGTAGCATTG 753–791 1.000 79.6
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CTGGTTGTAGCATTGGCACT 776–814 1.000 79.4
rps4-trnT-UGU_p1 rps4-trnT-UGU TAAGATCGCTTCCGGCTCTA CTCAGAGGTTAGAGCATCGC 905–971 1.000 84.2
rps4-trnT-UGU_p2 rps4-trnT-UGU TTTCTAAGATCGCTTCCGGC CTCAGAGGTTAGAGCATCGC 909–975 1.000 83.9
rps4-trnT-UGU_p3 rps4-trnT-UGU TAAGATCGCTTCCGGCTCTA TTGAGTTTGAGCCCGCTTAG 925–991 1.000 83.7
rps4-trnT-UGU_p4 rps4-trnT-UGU TAAGATCGCTTCCGGCTCTA ATGGTCATCGGTTCGATTCC 873–939 1.000 83.6
rps4-trnT-UGU_p5 rps4-trnT-UGU TTTCTAAGATCGCTTCCGGC TTGAGTTTGAGCCCGCTTAG 929–995 1.000 83.3
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1062–1125 1.000 83.3
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1070–1133 1.000 82.8
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1094–1157 1.000 82.5
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1102–1165 1.000 81.9
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA CAAATAGGGAAAGCCGGCTA ACCAATTTCGCCATATCCCC 1116–1179 1.000 81.7

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
Pterospermum heterophyllum PV738961.1 162857 View on NCBI ↗
Pterospermum kingtungense NC_042885.1 162929 View on NCBI ↗
Pterospermum truncatolobatum NC_054168.1 163158 View on NCBI ↗