Markers + reference

Calamus

6 species · Arecaceae · Arecales

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Species 6
Genome length 157–158 kb
Candidate markers 271
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 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
psbA LSC 1062 0.0012 1.00 39.0 yes View details
rps16-trnQ-UUG LSC 1157 0.0099 0.99 59.6 yes View details
trnC-GCA-petN LSC 1096 0.0080 1.00 61.0 yes View details
trnT-UGU-trnL-UAA LSC 1113 0.0131 0.95 72.0 yes View details
accD-psaI LSC 1033 0.0272 0.96 68.0 yes View details
petA-psbJ LSC 1011 0.0066 1.00 53.3 yes View details
rps3 LSC 657 0.0091 1.00 42.0 yes View details
rpl22-rps19 IRb 224 0.0347 0.95 76.8 yes View details
rps19 IRb 279 0.0012 1.00 23.1 yes View details
ndhF-rpl32 SSC 345 0.0168 1.00 56.6 yes View details
rps15-ycf1 SSC 320 0.0154 1.00 47.7 yes View details
rps19 IRa 279 0.0012 1.00 23.1 no View details
rps19-psbA LSC 252 0.0709 0.85 87.3 no View details
rpl16-rps3 LSC 146 0.0365 1.00 64.7 yes View details
atpF-atpH LSC 508 0.0089 0.99 62.3 yes View details
ccsA-ndhD SSC 225 0.0186 0.96 62.1 yes View details
rpoB-trnC-GCA LSC 1094 0.0041 1.00 61.3 yes View details
rpl32-trnL-UAG SSC 791 0.0069 1.00 60.1 yes View details
rps16 LSC 1146 0.0013 1.00 58.7 yes View details
trnS-GCU-trnG-UCC LSC 614 0.0051 1.00 58.0 yes View details
clpP LSC 2122 0.0053 0.99 57.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TGCTCCATTGTTTGATTCAACG TGGGAGCCCTTGAAAATTGA 1147 1.000 57.9
psbA_p2 psbA TGCTCCATTGTTTGATTCAACG GCTTGGGAGCCCTTGAAAAT 1150 1.000 57.6
psbA_p3 psbA GCTCCATTGTTTGATTCAACGA TGGGAGCCCTTGAAAATTGA 1146 1.000 57.4
psbA_p4 psbA GCTCCATTGTTTGATTCAACGA GCTTGGGAGCCCTTGAAAAT 1149 1.000 57.1
psbA_p5 psbA TGCTCCATTGTTTGATTCAACG TGGGAGCCCTTGAAAATTGAA 1147 1.000 55.2
rps16_p1 rps16 GCAAGAAAAAGGCAAATTGTGT ATACACACCGGTTGTTGAGC 1329 0.167 19.8
rps16_p2 rps16 ACAGCAAGAAAAAGGCAAATTG ATACACACCGGTTGTTGAGC 1332 0.167 17.6
rps16_p3 rps16 AGCAAGAAAAAGGCAAATTGTG ATACACACCGGTTGTTGAGC 1330 0.167 17.6
rps16_p4 rps16 CAGCAAGAAAAAGGCAAATTGT ATACACACCGGTTGTTGAGC 1331 0.167 17.6
rps16_p5 rps16 CAGCAAGAAAAAGGCAAATTGTG ATACACACCGGTTGTTGAGC 1331 0.167 17.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1228–1251 1.000 82.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1226–1249 1.000 82.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1234–1257 1.000 82.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1235–1258 1.000 82.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1210–1233 1.000 81.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 688–1134 1.000 54.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 691–1137 1.000 53.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 690–1136 1.000 53.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGAAGAAGCGGAGAGAGAGG ACGAATCACACTTTTACCACT 744–1190 1.000 52.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 689–1135 1.000 52.4
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG ATTTATGGACTGGTCGTGGC 603–636 1.000 84.0
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG GCTTTTGTTTGCGAATCCCT 577–610 1.000 80.9
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAAGGAA ATTTATGGACTGGTCGTGGC 575–608 1.000 79.8
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAAGGAAA ATTTATGGACTGGTCGTGGC 575–608 1.000 76.6
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAAGGAA GCTTTTGTTTGCGAATCCCT 549–582 1.000 76.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TAAAGGATTTGCAGTCCCCC 1242–1247 1.000 75.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA TAAAGGATTTGCAGTCCCCC 1162–1167 1.000 73.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TTTGTTGATCAGGCGACACC 1279–1284 1.000 73.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCCCTCATTTCCATTCCGG TAAAGGATTTGCAGTCCCCC 1163–1168 1.000 73.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG GACACCCGGATTTGAACTGG 1265–1270 1.000 72.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Calamus caryotoides NC_020365.1 157270 View on NCBI ↗
Calamus exilis NC_079714.1 158225 View on NCBI ↗
Calamus henryanus NC_079715.1 157536 View on NCBI ↗
Calamus jenkinsianus NC_067841.1 158029 View on NCBI ↗
Calamus tetradactylus NC_079772.1 157883 View on NCBI ↗
Calamus walkeri NC_067840.1 157106 View on NCBI ↗