Markers + reference

Streptosarcina

2 species · Hormidiellaceae · Hormidiellales

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Species 2
Genome length 167–199 kb
Candidate markers 287
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 287 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
orf490 Genome 1473 0.4359 0.97 81.3 yes View details
orf490-accD Genome 1944 0.3060 0.95 82.7 yes View details
rpl19-trnF(gaa) Genome 3153 0.4545 0.55 76.0 yes View details
minD-ccsA Genome 1245 0.3942 0.87 88.0 yes View details
trnF(gaa)-rpl19 Genome 3153 0.2750 0.03 57.7 yes View details
ycf12-trnL(uaa) Genome 1946 0.1969 0.93 97.1 yes View details
chlI-psbC Genome 1968 0.1470 0.96 85.0 yes View details
ndhB-minD Genome 1873 0.1941 0.98 82.3 yes View details
minD-ndhB Genome 1873 0.1941 0.98 82.3 yes View details
orf340-trnI(gau) Genome 831 0.3272 0.98 80.5 yes View details
trnI(gau)-orf340 Genome 831 0.3272 0.98 80.5 yes View details
trnQ(uug)-chlB Genome 334 0.0817 0.92 80.3 yes View details
trnV(uac)-trnMe(cau) Genome 676 0.0536 0.99 80.0 yes View details
ycf1-chlN Genome 606 0.0723 0.96 79.3 yes View details
orf340 Genome 1023 0.4143 1.00 79.0 yes View details
orf340 Genome 1023 0.4143 1.00 79.0 no 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
orf490_p1 orf490 GGGGACCGATCTAAGGAAGA TGTTCAAAGGCCTCTTGGTC 1973 0.500 59.2
orf490_p2 orf490 GGGGACCGATCTAAGGAAGA GGCCTCTTGGTCTATTGCTC 1965 0.500 59.0
orf490_p3 orf490 GTGTTTCCTTCTTTGCAGGC TGTTCAAAGGCCTCTTGGTC 1953 0.500 58.7
orf490_p4 orf490 GGGGACCGATCTAAGGAAGA GGGCTTGTCGAACATACTGT 1851 0.500 58.6
orf490_p5 orf490 GTGTTTCCTTCTTTGCAGGC GGCCTCTTGGTCTATTGCTC 1945 0.500 58.6
orf490-accD_p1 orf490-accD CATACCGGTCAGTCACAAGG CCATGCTGCCTCCCATAAAT 2900 0.500 59.9
orf490-accD_p2 orf490-accD CACCTGATCGATGAACTGCA CCATGCTGCCTCCCATAAAT 2701 0.500 59.8
orf490-accD_p3 orf490-accD TGCACCTGATCGATGAACTG CCATGCTGCCTCCCATAAAT 2703 0.500 59.8
orf490-accD_p4 orf490-accD ACCTGATCGATGAACTGCAC CCATGCTGCCTCCCATAAAT 2700 0.500 59.8
orf490-accD_p5 orf490-accD AGCCAGACTCAACCAGTAGT CCATGCTGCCTCCCATAAAT 2419 0.500 59.8
ycf12-trnL(uaa)_p1 ycf12-trnL(uaa) GTTCTGTCAGGTCCCCTAGT TTGAGACATAGGTTCGCACG 2092 0.500 59.4
ycf12-trnL(uaa)_p2 ycf12-trnL(uaa) TTCTGTCAGGTCCCCTAGTG TTGAGACATAGGTTCGCACG 2091 0.500 59.4
ycf12-trnL(uaa)_p3 ycf12-trnL(uaa) TGCACTCATCGTTCTGTCAG TTGAGACATAGGTTCGCACG 2102 0.500 59.4
ycf12-trnL(uaa)_p4 ycf12-trnL(uaa) AGCTAGCTGTTCTTGCACTC TTGAGACATAGGTTCGCACG 2115 0.500 59.2
ycf12-trnL(uaa)_p5 ycf12-trnL(uaa) CTAGTGATAGCCCTGCTTGC TTGAGACATAGGTTCGCACG 2077 0.500 58.9
chlI-psbC_p1 chlI-psbC GGTGCAAGAGAAGTTTAGCC GCAGGTTTTGAGAAGGGGAT 2080 0.500 48.0
chlI-psbC_p2 chlI-psbC GGTGCAAGAGAAGTTTAGCCA GCAGGTTTTGAGAAGGGGAT 2080 0.500 46.3
chlI-psbC_p3 chlI-psbC TGGTGCAAGAGAAGTTTAGCC GCAGGTTTTGAGAAGGGGAT 2081 0.500 46.3
chlI-psbC_p4 chlI-psbC GGTGCAAGAGAAGTTTAGCC GACACCGAACCCGTACTTTC 2053 0.500 45.1
chlI-psbC_p5 chlI-psbC GGTGCAAGAGAAGTTTAGCC AACCCGTACTTTCTATGGGC 2046 0.500 44.1
trnV(uac)-trnMe(cau)_p1 trnV(uac)-trnMe(cau) GAGCTAGAAGGCCACAGAAC TGAACCAATGACTTTCGCCT 831–843 1.000 81.5
trnV(uac)-trnMe(cau)_p2 trnV(uac)-trnMe(cau) GGGCTATACGGATTCGAACC TGAACCAATGACTTTCGCCT 803–815 1.000 81.2
trnV(uac)-trnMe(cau)_p3 trnV(uac)-trnMe(cau) ATGAGCTAGAAGGCCACAGA TGAACCAATGACTTTCGCCT 833–845 1.000 80.6
trnV(uac)-trnMe(cau)_p4 trnV(uac)-trnMe(cau) CGAACCGTAGACAATCTCGG TGAACCAATGACTTTCGCCT 789–801 1.000 80.5
trnV(uac)-trnMe(cau)_p5 trnV(uac)-trnMe(cau) AAGGCCACAGAACAAGGTTT TGAACCAATGACTTTCGCCT 824–836 1.000 80.4
trnQ(uug)-chlB_p1 trnQ(uug)-chlB AGCGGTAAAACACGTGACTT GTCTCCTAAAGGTGCATGCA 472–500 1.000 86.8
trnQ(uug)-chlB_p2 trnQ(uug)-chlB AAGCGGTAAAACACGTGACT GTCTCCTAAAGGTGCATGCA 473–501 1.000 86.7
trnQ(uug)-chlB_p3 trnQ(uug)-chlB GACTCATGCGTAGGAGGTTC GTCTCCTAAAGGTGCATGCA 451–479 1.000 85.7
trnQ(uug)-chlB_p4 trnQ(uug)-chlB AAGCGGTAAAACACGTGACT AGTCGTCTCCTAAAGGTGCA 477–505 1.000 84.7
trnQ(uug)-chlB_p5 trnQ(uug)-chlB AGCGGTAAAACACGTGACTT AGTCGTCTCCTAAAGGTGCA 476–504 1.000 84.7

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
Streptosarcina arenaria NC_082077.1 166784 View on NCBI ↗
Streptosarcina costaricana NC_082078.1 199199 View on NCBI ↗