Markers + reference

Artocarpus

8 species · Moraceae · Rosales

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Species 8
Genome length 160–161 kb
Candidate markers 271
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2 LSC 4182 0.0083 1.00 39.1 yes View details
trnT-UGU-trnL-UAA LSC 1269 0.0174 0.96 57.4 yes View details
rpl22 LSC 378 0.0162 1.00 39.1 yes View details
ycf1 IRb 987 0.0022 1.00 30.0 no View details
ndhF SSC 2277 0.0123 1.00 45.2 yes View details
ndhF-rpl32 SSC 1323 0.0208 0.99 56.8 yes View details
rpl32-trnL-UAG SSC 1716 0.0260 0.97 67.6 yes View details
ccsA-ndhD SSC 293 0.0291 0.98 54.2 yes View details
ycf1 SSC 5625 0.0133 1.00 42.3 yes View details
rpl2-trnH-GUG IRa 99 0.0440 0.96 62.1 no View details
rpl22-rps19 LSC 115 0.0416 0.94 60.5 yes View details
trnH-GUG-psbA LSC 428 0.0238 0.93 60.3 yes View details
psbC-trnS-UGA LSC 253 0.0281 1.00 59.2 yes View details
trnS-GCU-trnG-UCC LSC 709 0.0163 0.97 57.9 yes View details
ycf3-trnS-GGA LSC 726 0.0145 1.00 57.6 yes View details
matK-trnK-UUU LSC 800 0.0140 0.97 56.3 yes View details
trnF-GAA-ndhJ LSC 672 0.0109 1.00 54.5 yes View details
trnK-UUU-rps16 LSC 1047 0.0121 0.98 54.3 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 80 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 GGAAGTTATGCACGAGCGTA 498–550 1.000 86.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GGAAGTTATGCACGAGCGTA 512–564 1.000 85.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GGAAGTTATGCACGAGCGTA 511–563 1.000 85.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GGAAGTTATGCACGAGCGTA 513–565 1.000 85.9
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC GGAAGTTATGCACGAGCGTA 527–579 1.000 83.1
matK-trnK-UUU_p1 matK-trnK-UUU GACTCCCGAAAGATAAGTGGG AACGGTAGAGTACTCGGCTT 878–904 1.000 74.2
matK-trnK-UUU_p2 matK-trnK-UUU GACTCCCGAAAGATAAGTGGG ACGGTAGAGTACTCGGCTTT 877–903 1.000 74.2
matK-trnK-UUU_p3 matK-trnK-UUU ACTCCCGAAAGATAAGTGGG ACGGTAGAGTACTCGGCTTT 876–902 1.000 72.6
matK-trnK-UUU_p4 matK-trnK-UUU CTCCCGAAAGATAAGTGGGT AACGGTAGAGTACTCGGCTT 876–902 1.000 72.6
matK-trnK-UUU_p5 matK-trnK-UUU CTCCCGAAAGATAAGTGGGT ACGGTAGAGTACTCGGCTTT 875–901 1.000 72.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TATTTCAAAGAAGGCGGGGG 1140–1174 1.000 81.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTCAAAGAAGGCGGGGG 1139–1173 1.000 81.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TATTTCAAAGAAGGCGGGGG 1149–1183 1.000 80.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGAAGGCGGGGGTTTTTATG 1132–1162 0.500 59.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAAGGCGGGGGTTTTTATG 1131–1161 0.500 59.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 770–802 1.000 58.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 769–801 1.000 58.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 773–805 1.000 57.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 772–804 1.000 57.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 771–803 1.000 57.0
rpoC2_p1 rpoC2 TTCTCCCGTTTTCGTCCATT TGGGTCCATTCAACGTCAAC 243 1.000 79.3
rpoC2_p2 rpoC2 AATTCTCCCGTTTTCGTCCA TGGGTCCATTCAACGTCAAC 245 1.000 79.2
rpoC2_p3 rpoC2 TTCTCCCGTTTTCGTCCATT GGTCCATTCAACGTCAACGA 241 1.000 78.6
rpoC2_p4 rpoC2 AATTCTCCCGTTTTCGTCCA GGTCCATTCAACGTCAACGA 243 1.000 78.5
rpoC2_p5 rpoC2 TTCTCCCGTTTTCGTCCATT ATGGGTCCATTCAACGTCAA 244 1.000 77.8
psbC-trnS-UGA_p1 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GGTTGATAGCTCCGGTCTTG 403–414 1.000 80.1
psbC-trnS-UGA_p2 psbC-trnS-UGA GCTGCAGCAGGATTTGAAAA GGTTGATAGCTCCGGTCTTG 402–413 1.000 79.5
psbC-trnS-UGA_p3 psbC-trnS-UGA TAGGTCATTTATGGCACGCG GGTTGATAGCTCCGGTCTTG 437–448 1.000 79.4
psbC-trnS-UGA_p4 psbC-trnS-UGA AGCTGCAGCAGGATTTGAAA GATGGCCGAGTGGTTGATAG 414–425 1.000 79.4
psbC-trnS-UGA_p5 psbC-trnS-UGA TAGGTCATTTATGGCACGCG GATGGCCGAGTGGTTGATAG 448–459 1.000 78.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Artocarpus altilis NC_059002.1 160184 View on NCBI ↗
Artocarpus camansi NC_054247.1 160096 View on NCBI ↗
Artocarpus elasticus OR664166.1 160672 View on NCBI ↗
Artocarpus excelsus OR664167.1 160320 View on NCBI ↗
Artocarpus hypargyreus NC_057287.1 160952 View on NCBI ↗
Artocarpus nitidus subsp. lingnanensis PX696983.1 161009 View on NCBI ↗
Artocarpus petelotii NC_056286.1 161009 View on NCBI ↗
Artocarpus tonkinensis MZ379793.1 160987 View on NCBI ↗