Additional File 6 — RNA-Seq data for 6S RNA
Publicly available LAB RNA-Seq data was fetched from NCBI and mapped to the 6S RNA locus identified in this study. Strain and target genome assembly are shown in the upper left. The upper right shows the respective chromosome-id and position. Bioproject and SRA-ID are indicated on the right. Bioprojects are denoted by different colors to ease reading. Library size (mapped reads only) is indicated in the bottom left. Mapping and positions are shown relative to the 6S RNA locus (framed by dashed lines). The putative pRNA-site is highlighted in red. Upper pannel shows 6S RNA reads (+), lower panel shows anti-sense reads (-). In the latter, read starts at potential pRNA sites are indicated by filled bars to ease the determination of the pRNA start positions.
In case of paired-end sequencing data, only the first strand library was mapped. Note that many libraries were
not well described. Whenever issues were noticed, a note was added below each figure. E.g. “Looks like strand-
independent sequencing” indicates that the number of reads on + and - strands are about equal indicating that they
actually arose from the same strand. If no reads were found on the + strand, reads were “reverse complemented”.
Enterococcus faecalis ATCC 29212 (4)
+
-
NZ_CP008816.1: 956,503 .. 956,796
PRJEB12568: ERR1248401
Enterococcus faecalis (GCF_000742975.1)
Note: All reads reverse complemented Lib size: 1,796k
CTCGT
|
TGCCG
|
A
-30 21.0k
10.5k 5.2k 15.7k
50 25 12
37
TTTT
|
GAGAG
|
A
-20
GTAT
|
GCTAT
|
T
-10
ATAA
|
AGATG
|
G
1
TAAA
|
TCTGT
|
G
11
ATGT
|
ACGCG
|
T
21
TGTC
|
CTTTC
|
A
31
CTGT
|
GTTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
C
61
TAGG
|
GATCC
|
T
71
GCTT
|
GTATC
|
A
81
AAGT
|
TGGTA
|
A
91
CATG
|
CCTTT
|
T
101
CTTT
|
TGGTA
|
G
111
TTCA
|
ATACT
|
G
121
CGAT
|
CGAGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAT
|
CTTGC
|
G
151
GGTT
|
CAATA
|
C
161
TCTA
|
GGACG
|
A
171
TTAC
|
CGGCA
|
T
181
CGAC
|
GGATT
|
T
191
TACC
|
ATTTT
|
T
201
ATGT
|
AGATT
|
T
211
CTAA
|
ACAAT
|
T
221
TGCT
|
CTGGC
|
AAGT
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NZ_CP008816.1: 956,503 .. 956,796
PRJEB12568: ERR1248414
Enterococcus faecalis (GCF_000742975.1)
Note: All reads reverse complemented Lib size: 1,834k
10 reads 11 reads
CTCGT
|
TGCCG
|
A
-30 18.0k
9.0k 4.5k 13.5k
50 25 12
37
TTTT
|
GAGAG
|
A
-20
GTAT
|
GCTAT
|
T
-10
ATAA
|
AGATG
|
G
1
TAAA
|
TCTGT
|
G
11
ATGT
|
ACGCG
|
T
21
TGTC
|
CTTTC
|
A
31
CTGT
|
GTTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
C
61
TAGG
|
GATCC
|
T
71
GCTT
|
GTATC
|
A
81
AAGT
|
TGGTA
|
A
91
CATG
|
CCTTT
|
T
101
CTTT
|
TGGTA
|
G
111
TTCA
|
ATACT
|
G
121
CGAT
|
CGAGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAT
|
CTTGC
|
G
151
GGTT
|
CAATA
|
C
161
TCTA
|
GGACG
|
A
171
TTAC
|
CGGCA
|
T
181
CGAC
|
GGATT
|
T
191
TACC
|
ATTTT
|
T
201
ATGT
|
AGATT
|
T
211
CTAA
|
ACAAT
|
T
221
TGCT
|
CTGGC
|
AAGT
Found pRNA: GUU C GGU C AA Calculated pRNA: GUU C GGU C AA ...
...
TGTGTTGACCGAAC
+
-
NZ_CP008816.1: 956,503 .. 956,796
PRJEB12568: ERR1248418
Enterococcus faecalis (GCF_000742975.1)
Note: All reads reverse complemented Lib size: 1,318k
CTCGT
|
TGCCG
|
A
-30 14.0k
7.0k 3.5k 10.5k
10 5 2
7
TTTT
|
GAGAG
|
A
-20
GTAT
|
GCTAT
|
T
-10
ATAA
|
AGATG
|
G
1
TAAA
|
TCTGT
|
G
11
ATGT
|
ACGCG
|
T
21
TGTC
|
CTTTC
|
A
31
CTGT
|
GTTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
C
61
TAGG
|
GATCC
|
T
71
GCTT
|
GTATC
|
A
81
AAGT
|
TGGTA
|
A
91
CATG
|
CCTTT
|
T
101
CTTT
|
TGGTA
|
G
111
TTCA
|
ATACT
|
G
121
CGAT
|
CGAGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAT
|
CTTGC
|
G
151
GGTT
|
CAATA
|
C
161
TCTA
|
GGACG
|
A
171
TTAC
|
CGGCA
|
T
181
CGAC
|
GGATT
|
T
191
TACC
|
ATTTT
|
T
201
ATGT
|
AGATT
|
T
211
CTAA
|
ACAAT
|
T
221
TGCT
|
CTGGC
|
AAGT
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
proposed
proposed
proposed
Enterococcaceae
Enterococcus faecalis ATCC 29212 (4)
+
-
NZ_CP008816.1: 956,503 .. 956,796
PRJEB12568: ERR1248427
Enterococcus faecalis (GCF_000742975.1)
Note: All reads reverse complemented Lib size: 1,418k
CTCGT
|
TGCCG
|
A
-30 20.0k
10.0k 5.0k 15.0k
10 5 2
7
TTTT
|
GAGAG
|
A
-20
GTAT
|
GCTAT
|
T
-10
ATAA
|
AGATG
|
G
1
TAAA
|
TCTGT
|
G
11
ATGT
|
ACGCG
|
T
21
TGTC
|
CTTTC
|
A
31
CTGT
|
GTTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
C
61
TAGG
|
GATCC
|
T
71
GCTT
|
GTATC
|
A
81
AAGT
|
TGGTA
|
A
91
CATG
|
CCTTT
|
T
101
CTTT
|
TGGTA
|
G
111
TTCA
|
ATACT
|
G
121
CGAT
|
CGAGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAT
|
CTTGC
|
G
151
GGTT
|
CAATA
|
C
161
TCTA
|
GGACG
|
A
171
TTAC
|
CGGCA
|
T
181
CGAC
|
GGATT
|
T
191
TACC
|
ATTTT
|
T
201
ATGT
|
AGATT
|
T
211
CTAA
|
ACAAT
|
T
221
TGCT
|
CTGGC
|
AAGT
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
proposed
Enterococcus faecalis (13)
+
-
NZ_CP014949.1: 854,768 .. 855,061
PRJNA252696: SRR1391146
Enterococcus faecalis (GCF_001598635.1)
Note: Looks like strand-independed sequencing Lib size: 10,358k
CTCGT
|
TGCCG
|
A
-30 9.1k
4.5k 2.2k 6.9k
10k 5k 2.5k
7.5k
TTTT
|
GAGAG
|
A
-20
GTAT
|
GCTAT
|
T
-10
ATAA
|
AGATG
|
G
1
TAAA
|
TCTGT
|
G
11
ATGT
|
ACGCG
|
T
21
TGTC
|
CTTTC
|
A
31
CTGT
|
GTTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
C
61
TAGG
|
GATCC
|
T
71
GCTT
|
GTATC
|
A
81
AAGT
|
TGGTA
|
A
91
CATG
|
CCTTT
|
T
101
CTTT
|
TGGTA
|
G
111
TTCA
|
ATACT
|
G
121
CGAT
|
CGAGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAT
|
CTTGC
|
G
151
GGTT
|
CAATA
|
C
161
TCTA
|
GGACG
|
A
171
TTAC
|
CGGCA
|
T
181
CGAC
|
GGATT
|
T
191
TACC
|
ATTTT
|
T
201
ATGA
|
AGATT
|
T
211
CTAA
|
ACAAT
|
T
221
TGCT
|
CTGGC
|
AAGT
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NZ_CP014949.1: 854,768 .. 855,061
PRJNA279331: SRR1930106
Enterococcus faecalis (GCF_001598635.1)
Note: Looks like strand-independed sequencing Lib size: 7,286k
CTCGT
|
TGCCG
|
A
-30 310.0k
155.0k 77.5k 232.5k
309.3k 154.6k 77.3k
232k
TTTT
|
GAGAG
|
A
-20
GTAT
|
GCTAT
|
T
-10
ATAA
|
AGATG
|
G
1
TAAA
|
TCTGT
|
G
11
ATGT
|
ACGCG
|
T
21
TGTC
|
CTTTC
|
A
31
CTGT
|
GTTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
C
61
TAGG
|
GATCC
|
T
71
GCTT
|
GTATC
|
A
81
AAGT
|
TGGTA
|
A
91
CATG
|
CCTTT
|
T
101
CTTT
|
TGGTA
|
G
111
TTCA
|
ATACT
|
G
121
CGAT
|
CGAGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAT
|
CTTGC
|
G
151
GGTT
|
CAATA
|
C
161
TCTA
|
GGACG
|
A
171
TTAC
|
CGGCA
|
T
181
CGAC
|
GGATT
|
T
191
TACC
|
ATTTT
|
T
201
ATGA
|
AGATT
|
T
211
CTAA
|
ACAAT
|
T
221
TGCT
|
CTGGC
|
AAGT
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NZ_CP014949.1: 854,768 .. 855,061
PRJNA279331: SRR1930107
Enterococcus faecalis (GCF_001598635.1)
Note: Looks like strand-independed sequencing Lib size: 9,377k
CTCGT
|
TGCCG
|
A
-30 6.9k
3.4k 1.7k 5.1k
7.4k 3.7k 1.8k
5.5k
TTTT
|
GAGAG
|
A
-20
GTAT
|
GCTAT
|
T
-10
ATAA
|
AGATG
|
G
1
TAAA
|
TCTGT
|
G
11
ATGT
|
ACGCG
|
T
21
TGTC
|
CTTTC
|
A
31
CTGT
|
GTTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
C
61
TAGG
|
GATCC
|
T
71
GCTT
|
GTATC
|
A
81
AAGT
|
TGGTA
|
A
91
CATG
|
CCTTT
|
T
101
CTTT
|
TGGTA
|
G
111
TTCA
|
ATACT
|
G
121
CGAT
|
CGAGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAT
|
CTTGC
|
G
151
GGTT
|
CAATA
|
C
161
TCTA
|
GGACG
|
A
171
TTAC
|
CGGCA
|
T
181
CGAC
|
GGATT
|
T
191
TACC
|
ATTTT
|
T
201
ATGA
|
AGATT
|
T
211
CTAA
|
ACAAT
|
T
221
TGCT
|
CTGGC
|
AAGT
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
proposed proposed
proposed
Enterococcaceae
Enterococcus faecalis (13) +
-
NZ_CP014949.1: 854,768 .. 855,061
PRJNA315283: SRR3226959
Enterococcus faecalis (GCF_001598635.1)
Lib size: 4,771k
CTCGT
|
TGCCG
|
A
-30 71.0k
35.5k 17.7k 53.2k
10 5 2
7
TTTT
|
GAGAG
|
A
-20
GTAT
|
GCTAT
|
T
-10
ATAA
|
AGATG
|
G
1
TAAA
|
TCTGT
|
G
11
ATGT
|
ACGCG
|
T
21
TGTC
|
CTTTC
|
A
31
CTGT
|
GTTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
C
61
TAGG
|
GATCC
|
T
71
GCTT
|
GTATC
|
A
81
AAGT
|
TGGTA
|
A
91
CATG
|
CCTTT
|
T
101
CTTT
|
TGGTA
|
G
111
TTCA
|
ATACT
|
G
121
CGAT
|
CGAGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAT
|
CTTGC
|
G
151
GGTT
|
CAATA
|
C
161
TCTA
|
GGACG
|
A
171
TTAC
|
CGGCA
|
T
181
CGAC
|
GGATT
|
T
191
TACC
|
ATTTT
|
T
201
ATGA
|
AGATT
|
T
211
CTAA
|
ACAAT
|
T
221
TGCT
|
CTGGC
|
AAGT
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NZ_CP014949.1: 854,768 .. 855,061
PRJNA339105: SRR4292311
Enterococcus faecalis (GCF_001598635.1)
Note: Looks like strand-independed sequencing Lib size: 13,190k
CTCGT
|
TGCCG
|
A
-30 970.0k
485.0k 242.5k 727.5k
1001.8k 500.9k 250.4k
751.3k
TTTT
|
GAGAG
|
A
-20
GTAT
|
GCTAT
|
T
-10
ATAA
|
AGATG
|
G
1
TAAA
|
TCTGT
|
G
11
ATGT
|
ACGCG
|
T
21
TGTC
|
CTTTC
|
A
31
CTGT
|
GTTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
C
61
TAGG
|
GATCC
|
T
71
GCTT
|
GTATC
|
A
81
AAGT
|
TGGTA
|
A
91
CATG
|
CCTTT
|
T
101
CTTT
|
TGGTA
|
G
111
TTCA
|
ATACT
|
G
121
CGAT
|
CGAGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAT
|
CTTGC
|
G
151
GGTT
|
CAATA
|
C
161
TCTA
|
GGACG
|
A
171
TTAC
|
CGGCA
|
T
181
CGAC
|
GGATT
|
T
191
TACC
|
ATTTT
|
T
201
ATGA
|
AGATT
|
T
211
CTAA
|
ACAAT
|
T
221
TGCT
|
CTGGC
|
AAGT
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
proposed
proposed
Enterococcus faecium Aus0004 (6)
+
-
NC_017022.1: 2,529,576 .. 2,529,871
PRJNA497790: SRR8083528
Enterococcus faecium (GCF_000250945.1)
Note: All reads reverse complemented Lib size: 10,501k
TCTCA
|
TTGCT
|
C
-30 73.0k
36.5k 18.2k 54.7k
50 25 12
37
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NZ_CP012522.1: 1,158,967 .. 1,159,262
PRJNA497790: SRR8083529
Enterococcus faecium (GCF_001298485.1)
Note: All reads reverse complemented Lib size: 10,939k
TCTCA
|
TTGCT
|
C
-30 46.0k
23.0k 11.5k 34.5k
50 25 12
37
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NC_017022.1: 2,529,576 .. 2,529,871
PRJNA497790: SRR8083530
Enterococcus faecium (GCF_000250945.1)
Note: All reads reverse complemented Lib size: 11,996k
TCTCA
|
TTGCT
|
C
-30 65.0k
32.5k 16.2k 48.7k
10 5 2
7
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
proposed proposed
proposed
Enterococcaceae
Enterococcus faecium Aus0004 (6)
+
-
NC_017022.1: 2,529,576 .. 2,529,871
PRJNA497790: SRR8083531
Enterococcus faecium (GCF_000250945.1)
Note: All reads reverse complemented Lib size: 9,194k
TCTCA
|
TTGCT
|
C
-30 140.0k
70.0k 35.0k 105.0k
50 25 12
37
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NC_017022.1: 2,529,576 .. 2,529,871
PRJNA497790: SRR8083532
Enterococcus faecium (GCF_000250945.1)
Note: All reads reverse complemented Lib size: 11,517k
TCTCA
|
TTGCT
|
C
-30 60.0k
30.0k 15.0k 45.0k
10 5 2
7
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NC_017022.1: 2,529,576 .. 2,529,871
PRJNA497790: SRR8083533
Enterococcus faecium (GCF_000250945.1)
Note: All reads reverse complemented Lib size: 11,313k
TCTCA
|
TTGCT
|
C
-30 28.0k
14.0k 7.0k 21.0k
10 5 2
7
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
proposed proposed
proposed
Enterococcus faecium (7)
+
-
NZ_CP012522.1: 1,158,967 .. 1,159,262
PRJNA482869: SRR7592714
Enterococcus faecium (GCF_001298485.1)
Note: All reads reverse complemented Lib size: 30,513k
TCTCA
|
TTGCT
|
C
-30 13.0k
6.5k 3.2k 9.7k
10 5 2
7
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NZ_CP012522.1: 1,158,967 .. 1,159,262
PRJNA482869: SRR7592717
Enterococcus faecium (GCF_001298485.1)
Note: All reads reverse complemented Lib size: 17,955k
TCTCA
|
TTGCT
|
C
-30 5.9k
2.9k 1.4k 4.4k
10 5 2
7
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NZ_CP012522.1: 1,158,967 .. 1,159,262
PRJNA482869: SRR7592718
Enterococcus faecium (GCF_001298485.1)
Note: All reads reverse complemented Lib size: 17,050k
TCTCA
|
TTGCT
|
C
-30 5.5k
2.7k 1.3k 4.1k
10 5 2
7
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
proposed proposed
proposed
Enterococcaceae
Enterococcus faecium (7)
+
-
NZ_CP012522.1: 1,158,967 .. 1,159,262
PRJNA482869: SRR7592722
Enterococcus faecium (GCF_001298485.1)
Note: All reads reverse complemented Lib size: 19,093k
TCTCA
|
TTGCT
|
C
-30 4.2k
2.1k 1.0k 3.1k
10 5 2
7
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NZ_CP012522.1: 1,158,967 .. 1,159,262
PRJNA482869: SRR7592724
No reads on - strand Enterococcus faecium (GCF_001298485.1)
Note: All reads reverse complemented Lib size: 17,067k
TCTCA
|
TTGCT
|
C
-30 4.4k
2.2k 1.1k 3.2k
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
+
-
NZ_CP012522.1: 1,158,967 .. 1,159,262
PRJNA482869: SRR7592728
Enterococcus faecium (GCF_001298485.1)
Note: All reads reverse complemented Lib size: 20,068k
TCTCA
|
TTGCT
|
C
-30 3.2k
1.6k 0.8k 2.4k
10 5 2
7
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
proposed proposed
proposed
Enterococcus faecium (7)
+
-
NZ_CP012522.1: 1,158,967 .. 1,159,262
PRJNA497790: SRR8083529
Enterococcus faecium (GCF_001298485.1)
Note: All reads reverse complemented Lib size: 10,939k
TCTCA
|
TTGCT
|
C
-30 46.0k
23.0k 11.5k 34.5k
50 25 12
37
TTTT
|
TAAAT
|
T
-20
CATA
|
TGCTA
|
C
-10
TATA
|
GAGGT
|
G
1
GGAA
|
ATCTG
|
T
11
GATG
|
TTCGA
|
A
21
TTGT
|
CCTCT
|
T
31
TGTG
|
TGTTG
|
A
41
CCGA
|
ACATT
|
T
51
TTAT
|
TGATA
|
T
61
CTTG
|
GGACC
|
C
71
GTCT
|
TGTGT
|
C
81
ACTG
|
CTGGT
|
A
91
ACAT
|
GCCTT
|
A
101
TCAT
|
TTGGT
|
A
111
GTTC
|
GAAGC
|
T
121
ACGA
|
CCATG
|
G
131
GACC
|
CACCT
|
G
141
CTTG
|
AATTC
|
G
151
CGGG
|
ATCAA
|
T
161
ACTA
|
CAGGA
|
C
171
AAAC
|
AACGG
|
C
181
ATTA
|
ACGGA
|
G
191
ATTA
|
CCATC
|
T
201
TTTA
|
AAGAA
|
T
211
AAAG
|
CAATT
|
T
221
GCTC
|
TTGGC
|
A
231
AATT
|
G
Calculated pRNA: GUU C GGU C AA ...
TGTGTTGACCGAAC
proposed
Enterococcaceae
Tetragenococcus halophilus (3)
+
-
NZ_CP012047.1: 2,048,329 .. 2,048,624
PRJNA248252: SRR1295572
Tetragenococcus halophilus (GCF_001712815.1)
Note: Looks like strand-independed sequencing Lib size: 7,954k
TCTAT
|
TGCCA
|
C
-30 25.0k
12.5k 6.2k 18.7k
24.3k 12.1k 6k
18.2k
ATTT
|
GAAAG
|
A
-20
TTAT
|
GCTAC
|
T
-10
ATTG
|
ACTTG
|
G
1
GAAT
|
TCTGT
|
G
11
ATGT
|
ACGAG
|
T
21
TATC
|
CATTT
|
T
31
TAGT
|
ATTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
A
61
TTGG
|
GATCC
|
G
71
TTAG
|
GTGCC
|
A
81
ATGT
|
CAGCA
|
G
91
CACG
|
CCTTA
|
T
101
CATT
|
TGGTA
|
G
111
CTCA
|
AGACC
|
T
121
TGGC
|
CATGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAG
|
ACTTT
|
G
151
CGGG
|
ATCAA
|
T
161
ACTC
|
CAGGA
|
C
171
AATA
|
AACGG
|
C
181
ATCC
|
ACGGA
|
T
191
ATTA
|
CCCTT
|
T
201
TTTT
|
TAAAG
|
A
211
TAAA
|
ATCCC
|
T
221
TATC
|
AAAAA
|
T
231
GATA
|
A
Calculated pRNA: GUU C GGU C AA ...
AGTATTGACCGAAC
+
-
NZ_CP012047.1: 2,048,329 .. 2,048,624
PRJNA248252: SRR1296680
Tetragenococcus halophilus (GCF_001712815.1)
Note: Looks like strand-independed sequencing Lib size: 7,671k
TCTAT
|
TGCCA
|
C
-30 110.0k
55.0k 27.5k 82.5k
102.2k 51.1k 25.5k
76.7k
ATTT
|
GAAAG
|
A
-20
TTAT
|
GCTAC
|
T
-10
ATTG
|
ACTTG
|
G
1
GAAT
|
TCTGT
|
G
11
ATGT
|
ACGAG
|
T
21
TATC
|
CATTT
|
T
31
TAGT
|
ATTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
A
61
TTGG
|
GATCC
|
G
71
TTAG
|
GTGCC
|
A
81
ATGT
|
CAGCA
|
G
91
CACG
|
CCTTA
|
T
101
CATT
|
TGGTA
|
G
111
CTCA
|
AGACC
|
T
121
TGGC
|
CATGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAG
|
ACTTT
|
G
151
CGGG
|
ATCAA
|
T
161
ACTC
|
CAGGA
|
C
171
AATA
|
AACGG
|
C
181
ATCC
|
ACGGA
|
T
191
ATTA
|
CCCTT
|
T
201
TTTT
|
TAAAG
|
A
211
TAAA
|
ATCCC
|
T
221
TATC
|
AAAAA
|
T
231
GATA
|
A
Calculated pRNA: GUU C GGU C AA ...
AGTATTGACCGAAC
+
-
NZ_CP012047.1: 2,048,329 .. 2,048,624
PRJNA248252: SRR1296681
Tetragenococcus halophilus (GCF_001712815.1)
Note: Looks like strand-independed sequencing Lib size: 8,264k
TCTAT
|
TGCCA
|
C
-30 51.0k
25.5k 12.7k 38.2k
46.1k 23k 11.5k
34.6k
ATTT
|
GAAAG
|
A
-20
TTAT
|
GCTAC
|
T
-10
ATTG
|
ACTTG
|
G
1
GAAT
|
TCTGT
|
G
11
ATGT
|
ACGAG
|
T
21
TATC
|
CATTT
|
T
31
TAGT
|
ATTGA
|
C
41
CGAA
|
CATTT
|
T
51
TATT
|
GATAT
|
A
61
TTGG
|
GATCC
|
G
71
TTAG
|
GTGCC
|
A
81
ATGT
|
CAGCA
|
G
91
CACG
|
CCTTA
|
T
101
CATT
|
TGGTA
|
G
111
CTCA
|
AGACC
|
T
121
TGGC
|
CATGG
|
A
131
ACCC
|
ACCTG
|
C
141
TTAG
|
ACTTT
|
G
151
CGGG
|
ATCAA
|
T
161
ACTC
|
CAGGA
|
C
171
AATA
|
AACGG
|
C
181
ATCC
|
ACGGA
|
T
191
ATTA
|
CCCTT
|
T
201
TTTT
|
TAAAG
|
A
211
TAAA
|
ATCCC
|
T
221
TATC
|
AAAAA
|
T
231
GATA
|
A
Calculated pRNA: GUU C GGU C AA ...
AGTATTGACCGAAC
