Markers + reference

Abutilon

7 species · Malvaceae · Malvales

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Species 7
Genome length 159–160 kb
Candidate markers 269
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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 612 0.0467 1.00 89.4 yes View details
trnK-UUU-rps16 LSC 892 0.0176 0.98 60.7 yes View details
trnS-GCU-trnS-CGA LSC 826 0.0216 1.00 71.1 yes View details
trnT-UGU-trnL-UAA LSC 1361 0.0126 1.00 64.2 yes View details
ndhC-trnV LSC 1256 0.0156 0.98 63.2 yes View details
atpB-rbcL LSC 966 0.0121 1.00 61.2 yes View details
petA-psbJ LSC 1069 0.0153 1.00 62.9 yes View details
rpl16 LSC 1550 0.0082 0.99 53.9 yes View details
rps19 LSC 279 0.0041 1.00 28.5 yes View details
rpl32-ndhF SSC 1022 0.0137 1.00 57.3 yes View details
rpl2-trnH-GUG IRa 169 0.0556 0.93 79.4 no View details
rps19-rpl2 IRb 160 0.0665 0.93 73.3 yes View details
psbT-pbf1 LSC 74 0.0528 1.00 72.1 yes View details
rps4-trnT-UGU LSC 512 0.0137 1.00 68.0 yes View details
petN-psbM LSC 1157 0.0065 0.99 65.9 yes View details
pafII-cemA LSC 1054 0.0108 0.99 65.9 yes View details
petG-trnW-CCA LSC 159 0.0202 0.97 64.5 yes View details
trnR-UCU-atpA LSC 180 0.0194 1.00 63.7 yes View details
psbZ-trnG-GCC LSC 654 0.0091 1.00 62.9 yes View details
psaJ-rpl33 LSC 548 0.0160 1.00 62.0 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 TTCCCTCTAGACCTAGCTGC 635–707 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 649–721 1.000 90.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 648–720 1.000 90.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 650–722 1.000 90.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 684–756 1.000 88.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGAGCTCAACCCACAG 925–1115 0.857 80.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 ATACCATACCTCGGGGACAG AAAAGGAGCTCAACCCACAG 1489–1668 0.857 80.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 GATACCATACCTCGGGGACA AAAAGGAGCTCAACCCACAG 1632–1669 0.714 72.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 GATACCATACCTCGGGGACA CCCAATGAGCCGTTTATCGA 1771–1808 0.714 71.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 GATACCATACCTCGGGGACA TCCCAATGAGCCGTTTATCG 1772–1809 0.714 71.7
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 876–931 1.000 59.5
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 875–930 1.000 59.5
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA CGCACAACGGATTAGCAATC ACGAATCACACTTTTACCACT 891–946 1.000 58.6
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 879–934 1.000 58.4
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 878–933 1.000 58.4
trnS-CGA_p1 trnS-CGA CCAATTCCCCTGTTCGACAA TTCACTGAGGAAGCGGAAAC 1377–1436 1.000 85.0
trnS-CGA_p2 trnS-CGA CAAAAGTCGGCAAGGCTCTA TTCACTGAGGAAGCGGAAAC 1447–1506 0.857 77.9
trnS-CGA_p3 trnS-CGA CCAATTCCCCTGTTCGACAA CATTCACTGAGGAAGCGGAA 1413–1438 0.571 63.7
trnS-CGA_p4 trnS-CGA CAAAAGTCGGCAAGGCTCTA CATTCACTGAGGAAGCGGAA 1483–1508 0.571 62.8
trnS-CGA_p5 trnS-CGA ATTCCCCTGTTCGACAAAGG CATTCACTGAGGAAGCGGAA 1410–1435 0.571 62.8
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GAAACCCTTTTGAAAGACGCT 241–276 1.000 59.8
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAACCCTTTTGAAAGACGCT 240–275 1.000 58.0
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACGCTATTCAGGAACAAATGGA 225–260 1.000 57.3
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT GAAACCCTTTTGAAAGACGCT 276–311 1.000 56.6
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GAAACCCTTTTGAAAGACGC 241–276 1.000 55.7
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA ATTGCTACAGCGCTGTTCAT 1291–1320 1.000 80.6
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA TATTGCTACAGCGCTGTTCA 1292–1321 1.000 79.6
petN-psbM_p3 petN-psbM AGTAAGTCTTGCTTGGGCTG ATTGCTACAGCGCTGTTCAT 1297–1326 1.000 79.1
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TTGCTACAGCGCTGTTCATT 1290–1319 1.000 78.8
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TATTGCTACAGCGCTGTTCA 1298–1327 1.000 78.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Abutilon abutiloides PX334442.1 160301 View on NCBI ↗
Abutilon angulatum PX334443.1 160355 View on NCBI ↗
Abutilon geranioides PX334445.1 159458 View on NCBI ↗
Abutilon grandifolium PX334446.1 159735 View on NCBI ↗
Abutilon hirtum PX334447.1 160454 View on NCBI ↗
Abutilon indicum PP897811.1 160445 View on NCBI ↗
Abutilon longicuspe PX334444.1 160288 View on NCBI ↗