Markers + reference

Roya

2 species · Mesotaeniaceae · Zygnematales

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Species 2
Genome length 138–138 kb
Candidate markers 283
Primer pairs 100

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 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf2 Genome 5649 0.0005 1.00 52.8 yes View details
psbA-psbC Genome 913 0.0022 1.00 60.1 yes View details
petD Genome 1172 0.0000 1.00 29.5 yes View details
rps7-ndhB Genome 665 0.0075 1.00 63.1 yes View details
rpoB Genome 3189 0.0006 1.00 43.1 yes View details
trnQ-UUG-psbK Genome 218 0.0000 1.00 33.8 yes View details
ycf12-trnY-GUA Genome 195 0.0051 1.00 48.3 yes View details
trnS-GCU-ycf3 Genome 409 0.0049 1.00 57.6 yes View details
ndhH Genome 1188 0.0000 1.00 27.2 yes View details
ndhH-rps15 Genome 209 0.0144 1.00 60.8 yes View details
rrn4.5-orf230 Genome 673 0.0030 1.00 60.5 yes View details
orf230-rrn4.5 Genome 673 0.0030 1.00 60.5 yes View details
accD Genome 891 0.0011 1.00 59.4 yes View details
ndhK Genome 822 0.0012 1.00 59.4 yes View details
rpl16-rps3 Genome 1079 0.0009 1.00 59.3 yes View details
ndhA Genome 1098 0.0009 1.00 59.3 yes View details
ccsA Genome 966 0.0010 1.00 59.3 yes View details
atpB Genome 1482 0.0007 1.00 59.1 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
ycf2_p1 ycf2 ACATTTCATGCCAAAAATGCA AAATTGGATATATGCTTATTCTCA 291 1.000 40.3
ycf2_p2 ycf2 CATTTCATGCCAAAAATGCA AAATTGGATATATGCTTATTCTCA 290 1.000 40.3
ycf2_p3 ycf2 ACATTTCATGCCAAAAATGC AAATTGGATATATGCTTATTCTCA 291 1.000 40.3
ycf2_p4 ycf2 TGCCAAAAATGCATAGCTTA AAATTGGATATATGCTTATTCTCA 283 1.000 40.3
ycf2_p5 ycf2 TACATTTCATGCCAAAAATGCA AAATTGGATATATGCTTATTCTCA 292 1.000 40.3
trnG-UCC_p1 trnG-UCC TGAAAAACCTAAGAATTCACTTGT ACGATGGACGCTCTTCAATC 934 1.000 40.2
trnG-UCC_p2 trnG-UCC TGAAAAACCTAAGAATTCACTTGT GACGATGGACGCTCTTCAAT 935 1.000 40.2
trnG-UCC_p3 trnG-UCC TGAAAAACCTAAGAATTCACTTGT CGATGGACGCTCTTCAATCA 933 1.000 40.2
trnG-UCC_p4 trnG-UCC TGAAAAACCTAAGAATTCACTTGT TAGACGATGGACGCTCTTCA 937 1.000 40.2
trnG-UCC_p5 trnG-UCC TGAAAAACCTAAGAATTCACTTGT GTTAGACGATGGACGCTCTT 939 1.000 40.2
accD_p1 accD AAGATTCTTATGTAAAGGGGG CTAGCTCCTAAGGGGCTAGT 1004 1.000 40.1
accD_p2 accD AAAGATTCTTATGTAAAGGGGG CTAGCTCCTAAGGGGCTAGT 1005 1.000 40.1
accD_p3 accD AAGATTCTTATGTAAAGGGGG AACTAGCTCCTAAGGGGCTA 1006 1.000 40.1
accD_p4 accD AAGATTCTTATGTAAAGGGGG TAACTAGCTCCTAAGGGGCT 1007 1.000 40.1
accD_p5 accD AAAGATTCTTATGTAAAGGGGG AACTAGCTCCTAAGGGGCTA 1007 1.000 40.1
psbA-psbC_p1 psbA-psbC CACTTGGGCTGACATCATCA CATTTGTGGCATGCAGGAAG 1132–1133 1.000 79.2
psbA-psbC_p2 psbA-psbC ACACTTGGGCTGACATCATC CATTTGTGGCATGCAGGAAG 1133–1134 1.000 79.2
psbA-psbC_p3 psbA-psbC TTGGGCTGACATCATCAACC CATTTGTGGCATGCAGGAAG 1129–1130 1.000 78.9
psbA-psbC_p4 psbA-psbC CACTTGGGCTGACATCATCA ATTTGTGGCATGCAGGAAGA 1131–1132 1.000 78.7
psbA-psbC_p5 psbA-psbC ACACTTGGGCTGACATCATC ATTTGTGGCATGCAGGAAGA 1132–1133 1.000 78.7
petD_p1 petD TTGTTATGAGAGATTAAATGTTGT CGAAGCCCACATGCTAAGAA 1329 1.000 40.0
petD_p2 petD TTGTTATGAGAGATTAAATGTTGT TGAAAAGACGAAGCCCACAT 1337 1.000 40.0
petD_p3 petD TTGTTATGAGAGATTAAATGTTGT GAAAAGACGAAGCCCACATG 1336 1.000 40.0
petD_p4 petD TTGTTATGAGAGATTAAATGTTGT GACGAAGCCCACATGCTAAG 1331 1.000 40.0
petD_p5 petD TTGTTATGAGAGATTAAATGTTGT AGCCCACATGCTAAGAATCA 1326 1.000 40.0
rpl16-rps3_p1 rpl16-rps3 CCGTGTTGCTATTCCCTTCA CAAACTTTGCGTGCACAGAT 1253–1257 1.000 78.2
rpl16-rps3_p2 rpl16-rps3 CTTGAAGCCCGAATCTTCCA CAAACTTTGCGTGCACAGAT 1290–1294 1.000 78.2
rpl16-rps3_p3 rpl16-rps3 TTTCCCCGTGTTGCTATTCC CAAACTTTGCGTGCACAGAT 1258–1262 1.000 77.7
rpl16-rps3_p4 rpl16-rps3 CCGTGTTGCTATTCCCTTCA CGCGTACCTCTCCAAACTTT 1265–1269 1.000 77.5
rpl16-rps3_p5 rpl16-rps3 CTTGAAGCCCGAATCTTCCA CGCGTACCTCTCCAAACTTT 1302–1306 1.000 77.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Roya anglica NC_024168.1 138275 View on NCBI ↗
Roya obtusa NC_030315.1 138272 View on NCBI ↗