Markers + reference

Littledalea

4 species · Poaceae · Poales

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Species 4
Genome length 137–137 kb
Candidate markers 265
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 31.4 yes View details
psbA-trnK-UUU LSC 234 0.0000 1.00 21.8 yes View details
psbK-psbI LSC 414 0.0024 1.00 42.8 yes View details
trnT-GGU-trnE-UUC LSC 527 0.0019 1.00 44.5 yes View details
clpP LSC 651 0.0000 1.00 33.9 yes View details
clpP-psbB LSC 535 0.0121 1.00 51.8 yes View details
rps3 LSC 720 0.0042 1.00 47.6 yes View details
rpl32-trnL-UAG SSC 724 0.0041 1.00 47.7 yes View details
petB LSC 1398 0.0007 1.00 49.9 yes View details
ndhF-rpl32 SSC 945 0.0005 1.00 46.0 yes View details
trnG-UCC-trnT-GGU LSC 1240 0.0008 1.00 45.3 yes View details
matK-trnK-UUU LSC 681 0.0007 1.00 45.2 yes View details
petN-trnC-GCA LSC 933 0.0005 1.00 45.1 yes View details
trnT-UGU-trnL-UAA LSC 816 0.0006 1.00 45.1 yes View details
atpB-rbcL LSC 783 0.0006 1.00 45.1 yes View details
petA-psbJ LSC 817 0.0006 1.00 45.1 yes View details
psbE-petL LSC 1170 0.0004 1.00 45.1 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TGCTAGAACAAGATATTGGGCA AATACGTGTGCTTGGGAGTC 1183 1.000 59.2
psbA_p2 psbA TGGGCATTTCTGTCTTTTCT AATACGTGTGCTTGGGAGTC 1167 1.000 56.3
psbA_p3 psbA TGGGCATTTCTGTCTTTTCTT AATACGTGTGCTTGGGAGTC 1167 1.000 54.9
psbA_p4 psbA TTGGGCATTTCTGTCTTTTCT AATACGTGTGCTTGGGAGTC 1168 1.000 54.9
psbA_p5 psbA TGCTAGAACAAGATATTGGGCAT AATACGTGTGCTTGGGAGTC 1183 1.000 54.8
psbA-trnK-UUU_p1 psbA-trnK-UUU AAAACACCGAACCATCCGAT ACTAGTTCCGGGTTCGAGTC 373 1.000 71.8
psbA-trnK-UUU_p2 psbA-trnK-UUU AAAACACCGAACCATCCGAT GACTAGTTCCGGGTTCGAGT 374 1.000 71.8
psbA-trnK-UUU_p3 psbA-trnK-UUU AAAACACCGAACCATCCGAT ATCCGACTAGTTCCGGGTTC 378 1.000 71.3
psbA-trnK-UUU_p4 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT ACTAGTTCCGGGTTCGAGTC 302 1.000 71.0
psbA-trnK-UUU_p5 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT GACTAGTTCCGGGTTCGAGT 303 1.000 71.0
trnK-UUU_p1 trnK-UUU CAACCAAGTCAGCCCAAAGA AATGTTTTGACAGAAGCGCG 2745–2757 1.000 77.3
trnK-UUU_p2 trnK-UUU TCAACCAAGTCAGCCCAAAG AATGTTTTGACAGAAGCGCG 2746–2758 1.000 77.3
trnK-UUU_p3 trnK-UUU GTCAACCAAGTCAGCCCAAA AATGTTTTGACAGAAGCGCG 2747–2759 1.000 75.0
trnK-UUU_p4 trnK-UUU AACCAAGTCAGCCCAAAGAT AATGTTTTGACAGAAGCGCG 2744–2756 1.000 74.3
trnK-UUU_p5 trnK-UUU ACCAAGTCAGCCCAAAGATT AATGTTTTGACAGAAGCGCG 2743–2755 1.000 74.3
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT AATGTTTTGACAGAAGCGCG 876 1.000 69.4
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGG AATGTTTTGACAGAAGCGCG 876 1.000 67.5
matK-trnK-UUU_p3 matK-trnK-UUU CTCCTGAAAGAGAAGTGGGT AATGTTTTGACAGAAGCGCG 875 1.000 67.5
matK-trnK-UUU_p4 matK-trnK-UUU TCCTGAAAGAGAAGTGGGTAGA AATGTTTTGACAGAAGCGCG 874 1.000 62.8
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGTA AATGTTTTGACAGAAGCGCG 876 1.000 62.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTACTCCTCGCGTCCAG 557–558 1.000 79.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCCGTCCTGGGTCATTAGA 535–536 1.000 78.1
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTACTCCTCGCGTCCAG 554–555 1.000 77.4
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTTTTACTCCTCGCGTCCAG 555–556 1.000 77.4
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTTTTACTCCTCGCGTCCAG 556–557 1.000 77.4
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1330 1.000 40.9
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTAGCACGAG 1390 1.000 40.1
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1326 1.000 40.1
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1327 1.000 40.1
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1332 1.000 40.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Littledalea alaica NC_037519.1 136840 View on NCBI ↗
Littledalea przevalskyi NC_037497.1 136862 View on NCBI ↗
Littledalea racemosa NC_036350.1 136852 View on NCBI ↗
Littledalea tibetica MW218960.1 136852 View on NCBI ↗