# generated by Counters version 1.4.4, Mon May 17 20:21:47 2021
# /usr/local/bin/pyReadCounters.py -f /home/parallels/Documents/CRAC_Pipelines/test_code/test_run/novo_files/test_1.novo --gtf ../genome_files/Staphylococcus_aureus_usa300_FPR3757_1.3_with_intergenic.gtf -v -o /home/parallels/Documents/CRAC_Pipelines/test_code/test_run/pyReadCounters_blocks_nomuts_analyses/test_1_blocks_nomuts --mutations nomuts --blocks
# total number of reads	140134
# total number of mapped cDNAs:	117550
# total number of paired reads	56385
# total number of single reads	4780
# total number of reads overlapping genomic features	33969
# 	sense	29407
# 	anti-sense	4562
# feature	sense_overlap	anti-sense_overlap	cDNA count

## tRNA	9175	2
SAUSA300_0926	508	0	508
SAUSA300_1822	373	0	373
SAUSA300_1832	343	0	343
SAUSA300_1779	341	0	341
SAUSA300_1823	333	0	333
SAUSA300_0447	308	0	308
SAUSA300_1824	307	0	307
SAUSA300_1835	288	0	288
SAUSA300_1821	285	0	285
SAUSA300_1819	277	1	278
SAUSA300_1825	254	0	254
SAUSA300_2121	252	0	252
SAUSA300_1774	241	0	241
SAUSA300_1833	238	0	238
SAUSA300_0927	223	0	223
SAUSA300_1778	221	0	221
SAUSA300_0019	205	0	205
SAUSA300_1840	197	0	197
SAUSA300_1817	195	0	195
SAUSA300_1836	194	0	194
SAUSA300_0500	192	0	192
SAUSA300_1827	191	0	191
SAUSA300_2118	187	0	187
SAUSA300_1818	184	0	184
SAUSA300_2119	171	0	171
SAUSA300_1830	161	0	161
SAUSA300_1828	161	0	161
SAUSA300_1776	154	0	154
SAUSA300_1777	149	0	149
SAUSA300_1816	146	0	146
SAUSA300_2117	146	0	146
SAUSA300_1820	140	1	141
SAUSA300_1834	140	0	140
SAUSA300_1066	137	0	137
SAUSA300_1839	124	0	124
SAUSA300_1829	115	0	115
SAUSA300_1811	113	0	113
SAUSA300_1772	111	0	111
SAUSA300_0018	97	0	97
SAUSA300_1831	85	0	85
SAUSA300_0498	85	0	85
SAUSA300_1814	81	0	81
SAUSA300_1815	81	0	81
SAUSA300_1813	77	0	77
SAUSA300_2019	68	0	68
SAUSA300_2116	59	0	59
SAUSA300_1812	47	0	47
SAUSA300_1775	46	0	46
SAUSA300_1773	43	0	43
SAUSA300_2018	39	0	39
SAUSA300_2120	34	0	34
SAUSA300_0751	14	0	14
SAUSA300_1826	14	0	14

## rRNA	8842	0
rrsB	943	0	943
rrsE	903	0	903
rrlC	878	0	878
rrlB	862	0	862
rrsA	861	0	861
rrlD	845	0	845
rrsD	819	0	819
rrlE	790	0	790
rrlA	768	0	768
rrsC	721	0	721
rrfA	87	0	87
rrfE	86	0	86
rrfG	73	0	73
rrfC	73	0	73
rrfD	69	0	69
rrfB	64	0	64

## protein_coding	7389	839
treR	1171	0	1171
rpmB	442	0	442
SAUSA300_1585	327	0	327
SAUSA300_1337	86	0	86
SAUSA300_2481	83	0	83
fusA	75	0	75
gap_1	57	0	57
SAUSA300_1295	57	0	57
SAUSA300_0755	51	0	51
SAUSA300_1919	51	1	52
SAUSA300_1899	49	0	49
SAUSA300_0369	48	0	48
pgk	45	0	45
SAUSA300_0912	44	0	44
SAUSA300_0235	44	0	44
SAUSA300_1921	43	0	43
gltD	36	0	36
SAUSA300_0479	36	0	36
carB	34	0	34
rpsU	33	0	33
gpmI	33	0	33
glpD	33	0	33
ptsI	32	0	32
tuf	31	0	31
SAUSA300_2423	31	0	31
tsf	30	0	30
SAUSA300_0778	29	0	29
qoxA	29	0	29
SAUSA300_0932	28	0	28
ahpF	27	0	27
narK	27	0	27
rplS	26	0	26
glnR	26	0	26
eno	25	0	25
SAUSA300_0618	25	0	25
hup	24	0	24
SAUSA300_0933	24	40	64
SAUSA300_1005	23	0	23
SAUSA300_0278	23	0	23
SAUSA300_0795	23	0	23
ddh	23	0	23
SAUSA300_1988	22	0	22
rpsO	22	0	22
SAUSA300_0672	22	0	22
spxA	22	0	22
lpdA_1	22	0	22
SAUSA300_2507	21	0	21
SAUSA300_0529	21	0	21
rpoB	21	0	21
fabF	21	0	21
tig	21	0	21
rpmA	20	0	20
rpoC	20	0	20
tpiA	19	0	19
SAUSA300_1642	19	0	19
fba	19	0	19
ssb	18	0	18
SAUSA300_0777	18	0	18
rbfA	18	0	18
SAUSA300_1374	18	1	19
rpsJ	17	0	17
SAUSA300_1536	17	0	17
rpmF	16	0	16
rplD	16	0	16
qoxB	16	0	16
SAUSA300_0409	16	1	17
pyk	16	0	16
SAUSA300_2313	16	0	16
ribD	15	0	15
nhaC	15	3	18
ackA	15	0	15
SAUSA300_0374	15	10	25
valS	15	0	15
rpmG_1	15	0	15
SAUSA300_0980	15	0	15
SAUSA300_0922	15	0	15
SAUSA300_0489	15	0	15
atpA	15	0	15
ptsG_1	14	0	14
rplL	14	0	14
pyrE	14	0	14
rpsA	14	0	14
acpP	14	0	14
rplJ	14	0	14
codY	13	0	13
SAUSA300_1254	13	0	13
SAUSA300_2100	13	78	91
SAUSA300_2361	13	3	16
SAUSA300_2246	13	0	13
clpP	13	0	13
rpsS	13	0	13
SAUSA300_1086	13	0	13
mraZ	13	0	13
SAUSA300_1247	13	5	18
pbp2	13	0	13
ptsG_2	13	0	13
secY_1	13	0	13
tgt	13	0	13
SAUSA300_0703	13	0	13
atpB	12	0	12
purL	12	0	12
metK	12	0	12
SAUSA300_0471	12	0	12
SAUSA300_1179	12	0	12
SAUSA300_1665	11	0	11
hemG	11	0	11
ilvE	11	0	11
SAUSA300_0376	11	0	11
SAUSA300_1119	11	0	11
trxB	11	0	11
SAUSA300_0964	11	0	11
gyrA	11	0	11
tkt	11	0	11
pepF_1	11	0	11
SAUSA300_0639	11	0	11
atpH	11	0	11
leuS	11	0	11
agrA	10	3	13
gcvT	10	0	10
SAUSA300_1168	10	0	10
glnA	10	0	10
rpmE2	10	0	10
alaS	10	0	10
SAUSA300_1008	10	1	11
SAUSA300_0425	10	0	10
gltX	10	0	10
yajC	10	0	10
rplP	10	0	10
SAUSA300_1656	10	0	10
gpsA	10	0	10
SAUSA300_1099	10	4	14
ebpS	10	0	10
SAUSA300_0650	10	0	10
ssaA_1	9	1	10
SAUSA300_2258	9	0	9
SAUSA300_0438	9	0	9
SAUSA300_1351	9	0	9
fmtC	9	1	10
ftsZ	9	0	9
dnaI	9	0	9
SAUSA300_0474	9	0	9
glyS	9	0	9
recA	9	0	9
SAUSA300_1874	9	0	9
mecA	9	4	13
ftsA	9	0	9
SAUSA300_1261	9	0	9
rpsC	9	0	9
SAUSA300_1687	9	0	9
isaA	9	0	9
agrB	9	1	10
mreD	9	0	9
secF	9	0	9
sak	9	0	9
saeS	9	0	9
mqo_2	9	0	9
SAUSA300_1252	8	3	11
rplK	8	0	8
pfkA	8	0	8
SAUSA300_0619	8	0	8
SAUSA300_0937	8	0	8
rplA	8	0	8
SAUSA300_0360	8	0	8
agrC	8	2	10
purM	8	0	8
rplO	8	0	8
SAUSA300_2026	8	0	8
gpmA	8	1	9
atpG	8	0	8
pyrC	8	0	8
SAUSA300_0649	8	0	8
folD	8	0	8
gyrB	8	0	8
SAUSA300_0183	8	0	8
cyoE	8	0	8
efb	8	0	8
adk	8	0	8
asp23	8	0	8
prs	8	0	8
opuD	8	0	8
xpt	8	0	8
rplB	8	0	8
hemX	7	0	7
SAUSA300_0531	7	0	7
SAUSA300_0844	7	0	7
SAUSA300_0460	7	0	7
tyrS	7	0	7
SAUSA300_1232	7	0	7
rpsI	7	0	7
SAUSA300_1012	7	0	7
nrdI	7	0	7
SAUSA300_2037	7	0	7
sufD	7	0	7
purH	7	0	7
SAUSA300_1248	7	13	20
SAUSA300_1296	7	0	7
SAUSA300_2529	7	0	7
pyrR	7	0	7
rplU	7	0	7
serS	7	0	7
SAUSA300_1052	7	0	7
femA	7	0	7
pyrP	7	0	7
SAUSA300_1082	7	0	7
thrS	7	0	7
rpoE	7	0	7
SAUSA300_0716	7	0	7
hemA	7	0	7
atpD	7	0	7
pdhB	7	0	7
SAUSA300_0712	7	0	7
pyrF	7	0	7
SAUSA300_0857	6	0	6
gnd	6	0	6
SAUSA300_1858	6	1	7
SAUSA300_0989	6	1	7
parC	6	0	6
pdp	6	0	6
ndk	6	0	6
SAUSA300_0178	6	0	6
atpC	6	0	6
rplV	6	0	6
clpX	6	0	6
rpmG_2	6	0	6
rpsH	6	0	6
guaA	6	0	6
SAUSA300_0486	6	0	6
SAUSA300_1652	6	1	7
murC	6	0	6
SAUSA300_1026	6	0	6
fabH	6	0	6
rpsD	6	0	6
SAUSA300_0181	6	0	6
rpsL	6	0	6
infA	6	0	6
menA	6	1	7
SAUSA300_1698	6	0	6
SAUSA300_0631	6	5	11
rplM	6	0	6
pnpA	6	0	6
purD	6	0	6
rplC	6	0	6
SAUSA300_0234	6	0	6
atpF	6	1	7
trx	6	0	6
SAUSA300_1187	6	0	6
SAUSA300_0995	6	0	6
SAUSA300_0871	6	0	6
SAUSA300_0453	5	0	5
SAUSA300_1478	5	5	10
acnA	5	0	5
nupC	5	1	6
rpsB	5	0	5
SAUSA300_0571	5	0	5
SAUSA300_0252	5	0	5
gltT	5	0	5
SAUSA300_1697	5	0	5
SAUSA300_0693	5	0	5
SAUSA300_2077	5	0	5
clfA	5	0	5
SAUSA300_0733	5	0	5
trmD	5	0	5
SAUSA300_0027	5	0	5
deoD_2	5	4	9
dnaG	5	0	5
SAUSA300_0817	5	1	6
mnhD	5	0	5
SAUSA300_0821	5	0	5
dltD	5	1	6
pyrB	5	0	5
rexA	5	0	5
pgi	5	0	5
SAUSA300_1534	5	0	5
ribF	5	0	5
purB	5	0	5
dnaK	5	0	5
SAUSA300_2041	5	0	5
SAUSA300_1338	5	0	5
pdhA	5	0	5
rplW	5	0	5
SAUSA300_0602	5	0	5
SAUSA300_1904	5	3	8
msrA_2	5	0	5
SAUSA300_1916	5	0	5
SAUSA300_0030	5	0	5
SAUSA300_0640	5	0	5
gatB	5	0	5
nrdF	5	0	5
SAUSA300_0872	5	0	5
nuc_1	5	0	5
SAUSA300_2581	5	0	5
SAUSA300_1056	5	0	5
purA	5	0	5
trmE	5	0	5
SAUSA300_0558	5	0	5
lysS	5	0	5
rpoA	5	0	5
ppaC	5	0	5
SAUSA300_1797	5	0	5
recU	5	0	5
SAUSA300_2484	5	0	5
lipA	5	0	5
SAUSA300_0987	5	0	5
SAUSA300_0630	5	0	5
SAUSA300_0814	5	0	5
SAUSA300_1369	5	2	7
greA	5	0	5
SAUSA300_1346	5	0	5
dltA	5	0	5
SAUSA300_0231	4	0	4
SAUSA300_0620	4	0	4
lysP	4	0	4
SAUSA300_1258	4	0	4
aroK	4	0	4
typA	4	11	15
carA	4	0	4
rpsN_2	4	0	4
SAUSA300_1084	4	0	4
rplE	4	0	4
SAUSA300_2076	4	0	4
SAUSA300_1842	4	0	4
femB	4	0	4
rnc	4	0	4
dps	4	0	4
atl	4	0	4
SAUSA300_2418	4	0	4
glmU	4	0	4
fdhD	4	0	4
SAUSA300_0726	4	0	4
secA	4	0	4
pbuX	4	0	4
saeR	4	0	4
SAUSA300_1003	4	0	4
pyrG	4	0	4
lepA	4	0	4
rpsF	4	0	4
infB	4	0	4
ctaA	4	0	4
yfiA	4	0	4
SAUSA300_1653	4	1	5
pheT	4	0	4
oxaA	4	0	4
mscL	4	0	4
qoxC	4	0	4
nrdD	4	0	4
SAUSA300_0068	4	1	5
rpsM	4	0	4
mraW	4	0	4
SAUSA300_0833	4	0	4
ptsH	4	0	4
folC	4	0	4
clpC	4	0	4
SAUSA300_1915	4	0	4
purN	4	0	4
SAUSA300_0692	4	0	4
SAUSA300_2215	4	0	4
SAUSA300_0884	4	1	5
SAUSA300_1532	4	0	4
glcT	4	0	4
coaA	4	0	4
lytH	4	0	4
SAUSA300_1057	4	2	6
srrA	4	0	4
SAUSA300_0940	4	0	4
sarA	4	0	4
SAUSA300_0652	4	3	7
SAUSA300_2351	4	0	4
SAUSA300_0011	4	0	4
nirB	4	0	4
SAUSA300_0475	4	0	4
SAUSA300_1107	4	0	4
SAUSA300_0785	4	0	4
SAUSA300_1334	4	1	5
glyA	4	0	4
pbp3	4	0	4
SAUSA300_1695	4	0	4
rpsE	4	0	4
SAUSA300_0883	4	0	4
purR	4	0	4
SAUSA300_1573	4	0	4
SAUSA300_1648	4	0	4
polC	4	0	4
sufB	4	0	4
SAUSA300_0569	3	143	146
SAUSA300_0426	3	0	3
SAUSA300_1017	3	0	3
SAUSA300_1041	3	0	3
ileS	3	0	3
pyc	3	0	3
prsA	3	0	3
SAUSA300_0215	3	0	3
rplQ	3	0	3
SAUSA300_0658	3	0	3
SAUSA300_1863	3	0	3
SAUSA300_1494	3	1	4
SAUSA300_0839	3	0	3
SAUSA300_1785	3	3	6
gmk	3	0	3
sbi	3	0	3
SAUSA300_1583	3	0	3
SAUSA300_1183	3	0	3
SAUSA300_0916	3	0	3
modB	3	0	3
sufC	3	5	8
SAUSA300_2297	3	0	3
SAUSA300_2343	3	0	3
SAUSA300_2282	3	0	3
pyrD	3	0	3
guaB	3	0	3
SAUSA300_1304	3	0	3
SAUSA300_2133	3	0	3
rpoF	3	0	3
SAUSA300_1872	3	0	3
SAUSA300_2639	3	0	3
SAUSA300_1229	3	0	3
ksgA	3	0	3
adhE	3	0	3
alr	3	0	3
SAUSA300_1631	3	0	3
mnhA	3	0	3
SAUSA300_1495	3	1	4
rot	3	0	3
polA_2	3	0	3
fmt_1	3	0	3
SAUSA300_0816	3	0	3
SAUSA300_1373	3	0	3
rpmI	3	0	3
frp	3	0	3
cysK	3	0	3
SAUSA300_1058	3	0	3
rplF	3	0	3
SAUSA300_1375	3	0	3
SAUSA300_1851	3	0	3
SAUSA300_1902	3	1	4
topB	3	0	3
frr	3	0	3
SAUSA300_2068	3	0	3
SAUSA300_1802	3	0	3
oppA_1	3	0	3
rplX	3	0	3
SAUSA300_2330	3	2	5
SAUSA300_1158	3	0	3
SAUSA300_2264	3	1	4
SAUSA300_0024	3	0	3
rpsR	3	0	3
SAUSA300_0021	3	0	3
trkA	3	1	4
clpB	3	0	3
glk	3	1	4
SAUSA300_0482	3	0	3
SAUSA300_2328	3	0	3
prmA	3	0	3
glmM	3	0	3
SAUSA300_2040	3	0	3
SAUSA300_1572	3	0	3
tpx	3	0	3
rpsK	3	0	3
SAUSA300_2102	3	0	3
SAUSA300_1241	3	0	3
SAUSA300_1509	3	0	3
SAUSA300_2486	3	0	3
SAUSA300_0982	3	0	3
SAUSA300_0939	3	4	7
SAUSA300_0233	3	0	3
SAUSA300_0651	3	2	5
SAUSA300_1006	3	0	3
purC	3	0	3
SAUSA300_1462	3	0	3
fabG	3	1	4
SAUSA300_1685	3	0	3
recF	3	0	3
SAUSA300_1606	3	0	3
smpB	3	0	3
spsA	3	0	3
SAUSA300_1209	3	0	3
SAUSA300_1710	3	0	3
pyrH	3	0	3
rpsN	3	0	3
dnaA	3	0	3
SAUSA300_0598	3	0	3
murD	3	0	3
SAUSA300_0568	3	0	3
SAUSA300_1551	3	0	3
SAUSA300_1602	3	0	3
SAUSA300_1101	3	1	4
SAUSA300_2262	3	0	3
SAUSA300_0504	3	0	3
SAUSA300_1550	3	1	4
fur	3	0	3
purF	3	0	3
SAUSA300_1224	3	0	3
deoC_2	3	0	3
engA	3	0	3
SAUSA300_1784	3	1	4
smc	3	0	3
efp	3	0	3
nusG	3	0	3
purK	3	0	3
ftsK	3	0	3
SAUSA300_0813	3	0	3
SAUSA300_2349	3	0	3
recJ	3	0	3
galM	3	0	3
SAUSA300_0257	3	0	3
SAUSA300_1240	3	0	3
sufS	3	0	3
fmt_2	3	0	3
SAUSA300_1699	3	0	3
SAUSA300_1285	3	0	3
SAUSA300_1848	3	0	3
prfA	3	0	3
moaE	2	0	2
menD	2	0	2
SAUSA300_0648	2	0	2
sucC	2	0	2
uvrA	2	0	2
SAUSA300_2403	2	0	2
SAUSA300_1859	2	6	8
ychF	2	0	2
hemL_1	2	0	2
agrD	2	0	2
mnhC	2	0	2
rho	2	0	2
SAUSA300_2473	2	1	3
SAUSA300_2474	2	0	2
ilvA_1	2	0	2
SAUSA300_0355	2	0	2
SAUSA300_1971	2	0	2
adh	2	0	2
def_1	2	0	2
SAUSA300_0251	2	0	2
rplN	2	0	2
SAUSA300_0129	2	0	2
ureE	2	0	2
SAUSA300_2132	2	0	2
accC_1	2	0	2
rpsQ	2	0	2
SAUSA300_0899	2	0	2
SAUSA300_2112	2	0	2
SAUSA300_2384	2	0	2
SAUSA300_0924	2	0	2
msrA_1	2	1	3
SAUSA300_1674	2	0	2
dat	2	0	2
SAUSA300_0695	2	1	3
secG	2	0	2
ahpC	2	0	2
SAUSA300_0553	2	0	2
hutG	2	0	2
rpmC	2	0	2
murB	2	0	2
mqo_1	2	0	2
SAUSA300_0687	2	0	2
murA_1	2	0	2
rpoD	2	0	2
rplT	2	0	2
SAUSA300_0953	2	0	2
SAUSA300_0022	2	0	2
SAUSA300_0674	2	0	2
SAUSA300_0551	2	0	2
SAUSA300_1683	2	0	2
SAUSA300_0992	2	1	3
SAUSA300_1277	2	0	2
SAUSA300_0031	2	0	2
ispD	2	0	2
trpS	2	0	2
SAUSA300_0505	2	0	2
oppB_1	2	0	2
SAUSA300_0476	2	0	2
tetR	2	0	2
SAUSA300_2085	2	2	4
msrR	2	0	2
tagG	2	0	2
SAUSA300_1658	2	0	2
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SAUSA300_0593	2	0	2
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SAUSA300_2213	2	1	3
SAUSA300_2127	2	0	2
SAUSA300_0353	2	0	2
SAUSA300_0487	2	0	2
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SAUSA300_2331	2	0	2
SAUSA300_0582	2	0	2
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SAUSA300_1795	2	0	2
SAUSA300_1173	2	0	2
SAUSA300_0643	2	0	2
SAUSA300_0788	2	2	4
SAUSA300_0789	2	2	4
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SAUSA300_1556	2	0	2
SAUSA300_2265	2	0	2
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SAUSA300_2157	2	0	2
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SAUSA300_1496	2	0	2
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SAUSA300_1463	2	0	2
SAUSA300_1051	2	0	2
SAUSA300_2504	2	0	2
SAUSA300_2065	2	0	2
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SAUSA300_1236	2	0	2
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SAUSA300_2376	2	3	5
SAUSA300_2029	2	0	2
SAUSA300_2113	2	0	2
SAUSA300_1303	2	0	2
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SAUSA300_2562	2	0	2
SAUSA300_1701	2	0	2
SAUSA300_0834	2	0	2
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SAUSA300_0383	2	0	2
SAUSA300_0754	2	0	2
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SAUSA300_0372	2	1	3
SAUSA300_1497	2	0	2
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SAUSA300_2480	2	0	2
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SAUSA300_0430	2	0	2
SAUSA300_1318	2	0	2
SAUSA300_2267	2	2	4
SAUSA300_2266	2	1	3
SAUSA300_2357	2	0	2
SAUSA300_2147	2	0	2
SAUSA300_0218	2	0	2
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SAUSA300_0237	2	0	2
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SAUSA300_0561	2	0	2
SAUSA300_1574	2	0	2
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SAUSA300_2212	2	0	2
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SAUSA300_1518	2	0	2
SAUSA300_2128	2	0	2
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SAUSA300_0656	2	0	2
SAUSA300_2320	2	0	2
SAUSA300_2563	2	0	2
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SAUSA300_0911	2	1	3
SAUSA300_1729	2	0	2
SAUSA300_2337	2	0	2
SAUSA300_1112	2	0	2
SAUSA300_2103	2	0	2
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SAUSA300_1090	2	0	2
SAUSA300_0107	2	0	2
ffh	2	0	2
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SAUSA300_0565	2	0	2
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SAUSA300_1329	2	0	2
SAUSA300_1523	2	0	2
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SAUSA300_1298	2	0	2
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SAUSA300_0420	2	0	2
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SAUSA300_1474	2	0	2
SAUSA300_2094	2	0	2
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SAUSA300_1121	2	0	2
SAUSA300_1182	2	0	2
SAUSA300_0875	2	0	2
SAUSA300_0033	2	0	2
SAUSA300_1170	2	0	2
SAUSA300_0732	2	1	3
SAUSA300_0663	2	0	2
SAUSA300_0866	2	0	2
SAUSA300_1852	2	0	2
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SAUSA300_0427	2	0	2
SAUSA300_1085	2	0	2
SAUSA300_1703	2	0	2
SAUSA300_1333	2	0	2
SAUSA300_1238	2	0	2
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SAUSA300_0580	2	0	2
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SAUSA300_1314	2	0	2
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SAUSA300_2339	2	0	2
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SAUSA300_1054	2	0	2
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SAUSA300_1623	2	0	2
SAUSA300_0536	2	0	2
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SAUSA300_1155	2	0	2
SAUSA300_0023	2	0	2
SAUSA300_2537	2	0	2
SAUSA300_2472	2	0	2
SAUSA300_1460	2	0	2
SAUSA300_2452	2	0	2
SAUSA300_0858	2	0	2
SAUSA300_1455	2	0	2
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SAUSA300_1007	2	0	2
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SAUSA300_2643	1	0	1
SAUSA300_1747	1	34	35
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SAUSA300_0773	1	0	1
SAUSA300_0439	1	7	8
SAUSA300_2004	1	0	1
SAUSA300_1796	1	0	1
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SAUSA300_2497	1	0	1
SAUSA300_0746	1	0	1
SAUSA300_0408	1	9	10
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SAUSA300_1862	1	0	1
SAUSA300_0985	1	1	2
SAUSA300_1493	1	1	2
SAUSA300_1856	1	0	1
SAUSA300_0671	1	21	22
ureG	1	0	1
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SAUSA300_0931	1	0	1
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SAUSA300_0277	1	0	1
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SAUSA300_2021	1	0	1
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SAUSA300_1805	1	0	1
SAUSA300_2490	1	0	1
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SAUSA300_1584	1	0	1
SAUSA300_0668	1	0	1
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SAUSA300_0913	1	1	2
SAUSA300_0661	1	0	1
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SAUSA300_0728	1	0	1
SAUSA300_1566	1	0	1
SAUSA300_0945	1	6	7
SAUSA300_1897	1	0	1
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SAUSA300_1449	1	1	2
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SAUSA300_2261	1	3	4
SAUSA300_2578	1	0	1
SAUSA300_1984	1	1	2
SAUSA300_2269	1	0	1
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SAUSA300_2495	1	0	1
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SAUSA300_1607	1	0	1
SAUSA300_1483	1	0	1
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SAUSA300_2053	1	1	2
SAUSA300_0981	1	0	1
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SAUSA300_1515	1	0	1
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SAUSA300_2043	1	0	1
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SAUSA300_1197	1	1	2
SAUSA300_0706	1	0	1
SAUSA300_2344	1	0	1
SAUSA300_0542	1	1	2
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SAUSA300_0604	1	0	1
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SAUSA300_0664	1	0	1
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SAUSA300_1508	1	1	2
SAUSA300_1853	1	0	1
SAUSA300_0395	1	0	1
SAUSA300_1923	1	0	1
SAUSA300_1924	1	0	1
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SAUSA300_0688	1	0	1
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SAUSA300_1650	1	0	1
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SAUSA300_0681	1	0	1
SAUSA300_2505	1	0	1
SAUSA300_2232	1	1	2
SAUSA300_1736	1	0	1
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SAUSA300_1464	1	0	1
SAUSA300_1019	1	0	1
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SAUSA300_2030	1	0	1
SAUSA300_1067	1	0	1
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SAUSA300_2070	1	0	1
SAUSA300_1552	1	0	1
SAUSA300_0638	1	0	1
SAUSA300_2576	1	1	2
SAUSA300_2485	1	2	3
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SAUSA300_2583	1	0	1
SAUSA300_0014	1	0	1
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SAUSA300_0373	1	2	3
SAUSA300_0617	1	2	3
SAUSA300_0293	1	0	1
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SAUSA300_0761	1	0	1
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SAUSA300_1974	1	0	1
SAUSA300_0541	1	0	1
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SAUSA300_0441	1	0	1
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SAUSA300_1172	1	0	1
SAUSA300_0197	1	0	1
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SAUSA300_0013	1	0	1
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SAUSA300_2636	0	11	11
SAUSA300_0230	0	1	1
SAUSA300_1116	0	89	89
SAUSA300_1810	0	29	29
SAUSA300_0365	0	2	2
SAUSA300_2360	0	12	12
tnp	0	45	45
SAUSA300_0936	0	2	2
SAUSA300_2296	0	1	1
SAUSA300_0753	0	13	13
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SAUSA300_1309	0	6	6
SAUSA300_2417	0	4	4
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SAUSA300_1106	0	3	3
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SAUSA300_0540	0	2	2
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SAUSA300_1909	0	1	1
SAUSA300_0028	0	2	2
SAUSA300_0422	0	1	1
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SAUSA300_2445	0	1	1
SAUSA300_1372	0	1	1
SAUSA300_2382	0	1	1
SAUSA300_2368	0	1	1
proC	0	1	1

## sRNA	3233	633
4.5S	1169	0	1169
6S	326	0	326
srn_1510_rsaA	142	0	142
tmRNA	123	0	123
srn_2740_Teg108	108	0	108
srn_3840_sprG1	92	11	103
srn_4830_Sau6072	83	0	83
srn_4100_sprG3	78	8	86
srn_3460_Sau5949	58	0	58
RNAseP	57	0	57
srn_3580_SprA1	51	6	57
srn_3800_sprD	48	0	48
srn_2240_sprF2	40	18	58
srn_3820_SprX	40	0	40
srn_2230_sprG2	37	34	71
srn_3370_RsaOW5	34	0	34
srn_0960_Teg147	34	0	34
srn_2720_Teg104	33	0	33
srn_1320_sRNA117	32	0	32
srn_1960_rsaOL	29	0	29
srn_4480_Teg126	23	0	23
srn_3910_RNAIII	22	0	22
srn_2030_Teg52	22	0	22
srn_2950_Teg6	21	0	21
srn_4890_Teg134	20	0	20
srn_4680_Sau19	18	1	19
srn_3080_Teg66	16	0	16
srn_3510_Teg74	15	0	15
srn_2250_sprG4	15	31	46
srn_4340_Teg23	15	0	15
srn_4160_Sau25	14	0	14
srn_4520_RsaX20	13	3	16
srn_2200_Sau6053	13	0	13
srn_1910_rsaH	11	0	11
srn_3830_sprF1	11	23	34
srn_3550_Teg75	11	0	11
srn_3150_Teg83	10	0	10
srn_0890_sRNA71	10	0	10
srn_2347	10	0	10
srn_2550_Teg80	10	0	10
srn_0580_Sau6569	10	0	10
srn_3490_RsaOE	10	0	10
srn_4090_sprF3	9	27	36
srn_3300_Teg70	9	0	9
srn_1590_rsaC	9	0	9
srn_2880_RsaOQ	9	0	9
srn_2130_rsaE	9	0	9
srn_2620_Teg61	8	0	8
srn_0860_RsaOB	8	0	8
srn_1080_RsaX05	8	0	8
srn_2850_Teg112	8	0	8
srn_0930_Teg76	8	0	8
srn_1070_Sau41	7	0	7
srn_2070_Sau6851	6	0	6
srn_3590_sprAs1	6	9	15
srn_1100_Sau6054	6	0	6
srn_3390_Teg7	6	0	6
srn_2330_Sau11	6	0	6
srn_0030_Teg35	6	0	6
srn_3330_Teg71	6	0	6
srn_2350_rsaOP	6	0	6
srn_3160_RsaOD	6	0	6
srn_1350_Teg45	5	0	5
srn_2610_Sau24	5	0	5
srn_3320_sRNA264	5	0	5
srn_1640_rsaD	5	0	5
srn_2680_Sau6041	4	0	4
srn_3765	4	0	4
srn_1490_Sau6477	4	0	4
srn_2580_Teg103	4	1	5
srn_3310_sRNA263	3	0	3
srn_0440_rsaK	3	0	3
srn_1660_sRNA140	3	0	3
srn_9340_sRNA287	3	0	3
srn_4370_sRNA355	3	0	3
srn_1420_Sau60	3	0	3
srn_3480_sRNA275	3	0	3
srn_4015_tsr31	3	0	3
srn_2700_Teg62	3	0	3
srn_1500_Sau6667	3	0	3
srn_3260_Teg69	3	0	3
srn_0050_Teg1	3	0	3
srn_3270_sRNA259	3	0	3
srn_2590_Sau46	3	0	3
srn_9348	3	0	3
srn_1410_Teg77	3	0	3
srn_3470_sRNA274	3	0	3
srn_4540_sprAs2	3	0	3
srn_3780_Teg13	2	0	2
srn_4660_sRNA380	2	0	2
srn_2530_sRNA209	2	0	2
srn_1670_Teg20as	2	3	5
srn_3810_Teg124	2	0	2
srn_4550_sprA2	2	3	5
srn_4050_artR	2	0	2
srn_5010_Teg33	2	0	2
srn_0010_sRNA412	2	0	2
srn_1810_Teg51	2	0	2
srn_2460_Teg58	2	0	2
srn_3770_Teg122	2	0	2
srn_2080_Sau6851	2	0	2
srn_4330_Teg36as	1	4	5
srn_2450_Sau6229	1	0	1
srn_1790_sRNA150	1	0	1
srn_9525_tsr26	1	0	1
srn_5070_RsaX25	1	0	1
srn_2480_sRNA205	1	0	1
srn_4400_sRNA357	1	0	1
srn_2540_sRNA210	1	0	1
srn_1540_Teg48	1	0	1
srn_5110_sRNA411	1	0	1
srn_4260_Sau30	1	0	1
srn_1450_Sau6057	1	0	1
srn_2520_Teg60	1	0	1
srn_1520_Sau76	1	0	1
srn_4390_rsaOG	1	0	1
srn_2560_sRNA212	1	0	1
srn_1690_sRNA143	1	0	1
srn_3950_Teg16	1	0	1
srn_1620_Sau6836	1	0	1
srn_3360_sRNA267	1	0	1
srn_0380_Teg140	1	0	1
srn_3190_Teg68	1	0	1
srn_2260_sprF4	1	0	1
srn_3790_sRNA301	1	0	1
srn_3220_sRNA254	1	0	1
srn_3340_Teg72	1	0	1
srn_3500_sRNA277	1	0	1
srn_1060_Teg149	1	0	1
srn_4790_sRNA387	1	0	1
srn_0170_Teg9as	1	0	1
srn_3630_Sau69	1	0	1
srn_5120_Sau5995	1	0	1
srn_2910_Teg63	1	0	1
srn_1270_Teg44	1	0	1
srn_4950_sRNA397	1	0	1
srn_3060_sRNA243	1	0	1
srn_3540_sRNA280	1	0	1
srn_3960_sRNA323	0	147	147
srn_1090_Teg19as	0	5	5
srn_3040_Sau50	0	19	19
srn_9490_sRNA337	0	45	45
srn_4140_sRNA338	0	29	29
srn_0880_Sau5971	0	48	48
srn_4670_RsaOT	0	12	12
srn_3020_Teg65	0	23	23
srn_2345_tsr19	0	1	1
srn_9630_tsr30	0	2	2
srn_1250_sRNA110	0	5	5
srn_2180_sRNA188	0	1	1
srn_1580_sbrC	0	9	9
srn_4920_Sau39	0	2	2
srn_1230_sRNA108	0	2	2
srn_1210_sRNA106	0	7	7
srn_0570_sRNA35	0	1	1
srn_4800_rsaOU	0	10	10
srn_9460_sRNA316	0	1	1
srn_3740_Sau6492	0	3	3
srn_3070_Sau6889	0	1	1
srn_0950_Sau63	0	6	6
srn_2630_sRNA217	0	1	1
srn_0650_sRNA42	0	1	1
srn_0170_srn_0120_Teg9as_Teg6as	0	4	4
srn_1430_sRNA126	0	4	4
srn_9110_sRNA75	0	1	1
srn_1220_sRNA107	0	1	1
srn_4270_sRNA347	0	2	2
srn_4010_sRNA327	0	3	3
srn_1390_sRNA123	0	1	1
srn_1505_S204	0	2	2
srn_4280_Sau73	0	2	2
srn_2870_Sau28	0	3	3
srn_1930_rsaOF	0	11	11
srn_4110_sRNA335	0	1	1
srn_0940_Sau6356	0	1	1
srn_3100_sRNA246	0	1	1
srn_2650_sRNA218	0	1	1
srn_1890_sRNA161	0	3	3
srn_2348	0	4	4
srn_1460_sRNA128	0	2	2
srn_2670_Sau12	0	2	2
srn_2570_sRNA213	0	3	3
srn_3140_Teg151	0	1	1
srn_1260_Sau62	0	1	1
srn_2860_sRNA229	0	1	1
srn_1400_sRNA124	0	1	1
srn_4640_Sau6488	0	1	1
srn_2320_sRNA195	0	1	1
srn_0070_sRNA4	0	1	1
srn_0600_sRNA38	0	1	1
srn_2810_Sau6742	0	1	1
srn_4060_Sau6723	0	2	2
srn_0120_Teg6as	0	2	2
srn_3350_sRNA266	0	1	1
srn_1010_sRNA89	0	2	2
srn_1020_sRNA90	0	1	1
srn_0670_Sau6994	0	1	1

## intergenic	645	3088
INT_gltD_SAUSA300_0447	78	0	78
INT_SAUSA300_0498_rrsB	73	0	73
INT_SAUSA300_0018_SAUSA300_0019	66	0	66
INT_rrsB_SAUSA300_0500	41	0	41
INT_rrlA_rrfA	31	0	31
INT_SAUSA300_1732_SAUSA300_1733	30	0	30
INT_SAUSA300_0500_rrlB	28	0	28
INT_recR_rrsA	27	0	27
INT_lysS_rrfG	23	0	23
INT_SAUSA300_0447_treP	22	0	22
INT_smpB_ssrA_tmRNA	22	0	22
INT_SAUSA300_0019_SAUSA300_0020	18	0	18
INT_rrlB_rrfB	17	0	17
INT_SAUSA300_0392_srn_0960_Teg147	17	0	17
INT_purA_SAUSA300_0018	15	0	15
INT_rrfG_SAUSA300_0498	15	0	15
INT_rrfA_SAUSA300_0458	14	0	14
INT_rrsA_rrlA	13	0	13
INT_rrfB_srn_1330_sRNA118	11	0	11
INT_srn_2950_Teg6_SAUSA300_1286	8	0	8
INT_SAUSA300_1693_srn_3460_Sau5949	6	0	6
INT_carB_pyrF	4	0	4
INT_ilvE_SAUSA300_0540	3	0	3
INT_SAUSA300_0393	3	2	5
INT_SAUSA300_0402_SAUSA300_0403	3	0	3
INT_ybaK_SAUSA300_0683	3	0	3
INT_rpsO_pnpA	3	0	3
INT_rpoB_rpoB	3	0	3
INT_tsf_pyrH	3	0	3
INT_SAUSA300_2423_srn_4680_Sau19	3	0	3
INT_pgk_tpiA	2	0	2
INT_srn_4680_Sau19_SAUSA300_2424	2	2	4
INT_SAUSA300_1299_brnQ	2	0	2
INT_rplL_SAUSA300_0526	2	0	2
INT_SAUSA300_1819_SAUSA300_1820	1	54	55
INT_SAUSA300_1064_srn_2520_Teg60	1	0	1
INT_srn_9500_sRNA368_sbi	1	0	1
INT_SAUSA300_0930_SAUSA300_0931	1	0	1
INT_SAUSA300_2639_SAUSA300_2640	1	0	1
INT_SAUSA300_0137_deoD_1	1	0	1
INT_pyrR_pyrP	1	0	1
INT_cap5C_cap5E	1	0	1
INT_frr_uppS	1	0	1
INT_ffh_rpsP	1	0	1
INT_rbfA_truB	1	0	1
INT_SAUSA300_0584_SAUSA300_0585	1	0	1
INT_pdhB_SAUSA300_0995	1	0	1
INT_opuD_acnA	1	0	1
INT_scdA_SAUSA300_0254	1	0	1
INT_SAUSA300_1863_SAUSA300_1864	1	0	1
INT_cidA_SAUSA300_2480	1	0	1
INT_SAUSA300_0571_mvk	1	0	1
INT_rex_vga	1	0	1
INT_SAUSA300_0871_SAUSA300_0872	1	0	1
INT_rpsN_guaC	1	0	1
INT_srn_3770_Teg122_srn_3780_Teg13	1	0	1
INT_rot_SAUSA300_1710	1	0	1
INT_rpmG_rpsN	1	0	1
INT_SAUSA300_0022_SAUSA300_0023	1	0	1
INT_SAUSA300_0234_SAUSA300_0235	1	0	1
INT_ssrA_tmRNA_SAUSA300_0767	1	0	1
INT_SAUSA300_1725_SAUSA300_1726	1	0	1
INT_SAUSA300_0814_SAUSA300_0816	1	0	1
INT_SAUSA300_1182_SAUSA300_1183	1	0	1
INT_menE_SAUSA300_1738	1	0	1
INT_SAUSA300_0129_SAUSA300_0130	1	0	1
INT_SAUSA300_1084_SAUSA300_1085	1	0	1
INT_SAUSA300_0403_srn_1010_sRNA89	1	0	1
INT_SAUSA300_1773_SAUSA300_1774	0	69	69
INT_SAUSA300_1816_SAUSA300_1817	0	113	113
INT_SAUSA300_0750_SAUSA300_0751	0	7	7
INT_SAUSA300_1829_SAUSA300_1830	0	93	93
INT_SAUSA300_1821_SAUSA300_1822	0	79	79
INT_SAUSA300_1822_SAUSA300_1823	0	110	110
INT_SAUSA300_1823_SAUSA300_1824	0	162	162
INT_rrfE_rrlE	0	8	8
INT_SAUSA300_1777_SAUSA300_1778	0	88	88
INT_SAUSA300_1812_SAUSA300_1813	0	69	69
INT_SAUSA300_1824_SAUSA300_1825	0	49	49
INT_SAUSA300_1066_srn_2540_sRNA210	0	9	9
INT_SAUSA300_2120_SAUSA300_2121	0	71	71
INT_SAUSA300_1820_SAUSA300_1821	0	90	90
INT_SAUSA300_1818_SAUSA300_1819	0	72	72
INT_SAUSA300_2019_SAUSA300_2020	0	13	13
INT_SAUSA300_2635_srn_5110_sRNA411_SAUSA300_2636	0	11	11
INT_SAUSA300_0926_SAUSA300_0927	0	86	86
INT_SAUSA300_1776_SAUSA300_1777	0	111	111
INT_SAUSA300_0925_SAUSA300_0926	0	86	86
INT_SAUSA300_1839_SAUSA300_1840	0	61	61
INT_SAUSA300_1834_SAUSA300_1835	0	72	72
INT_SAUSA300_1204_srn_2740_Teg108	0	12	12
INT_SAUSA300_1835_SAUSA300_1836	0	45	45
INT_SAUSA300_1778_SAUSA300_1779	0	48	48
INT_srn_3590_sprAs1_SAUSA300_1749	0	5	5
INT_SAUSA300_1779_SAUSA300_1780	0	58	58
INT_SAUSA300_1833_SAUSA300_1834	0	107	107
INT_SAUSA300_1814_SAUSA300_1815	0	33	33
INT_SAUSA300_1828_SAUSA300_1829	0	68	68
INT_SAUSA300_2117_SAUSA300_2118	0	53	53
INT_SAUSA300_1832_SAUSA300_1833	0	94	94
INT_SAUSA300_1831_SAUSA300_1832	0	85	85
INT_SAUSA300_1826_SAUSA300_1827	0	13	13
INT_SAUSA300_1836_rrfC	0	39	39
INT_SAUSA300_1817_SAUSA300_1818	0	28	28
INT_SAUSA300_1827_SAUSA300_1828	0	37	37
INT_SAUSA300_2116_SAUSA300_2117	0	47	47
INT_SAUSA300_1772_SAUSA300_1773	0	35	35
INT_srn_2530_sRNA209_SAUSA300_1066	0	37	37
INT_SAUSA300_1813_SAUSA300_1814	0	26	26
INT_SAUSA300_1252_glcT	0	1	1
INT_SAUSA300_1774_SAUSA300_1775	0	43	43
INT_SAUSA300_2118_SAUSA300_2119	0	32	32
INT_SAUSA300_1840_rrsC	0	26	26
INT_SAUSA300_2119_SAUSA300_2120	0	27	27
INT_rrlC_SAUSA300_1839	0	16	16
INT_rrsC_SAUSA300_1842	0	8	8
INT_SAUSA300_2140_asp23	0	2	2
INT_SAUSA300_2422_SAUSA300_2423	0	7	7
INT_SAUSA300_2121_rrfE	0	39	39
INT_SAUSA300_2497_crtN	0	1	1
INT_SAUSA300_1775_SAUSA300_1776	0	32	32
INT_SAUSA300_1815_SAUSA300_1816	0	18	18
INT_tnp_SAUSA300_2116	0	4	4
INT_rrfC_rrlC	0	9	9
INT_rrsD_SAUSA300_2018	0	25	25
INT_SAUSA300_1825_SAUSA300_1826	0	30	30
INT_SAUSA300_1924_srn_3830_sprF1	0	1	1
INT_SAUSA300_0148_adhE	0	8	8
INT_ilvA_rrfD	0	11	11
INT_rrlE_rrsE	0	23	23
INT_SAUSA300_1543_lepA	0	1	1
INT_srn_2975_tsr25_SAUSA300_1309	0	34	34
INT_SAUSA300_2050_SAUSA300_2051	0	9	9
INT_srn_3380_Teg32as_SAUSA300_1811	0	7	7
INT_rrlD_rrsD	0	45	45
INT_SAUSA300_1811_SAUSA300_1812	0	12	12
INT_SAUSA300_1830_SAUSA300_1831	0	34	34
INT_SAUSA300_1294_SAUSA300_1295	0	3	3
INT_srn_3840_sprG1_SAUSA300_1925	0	2	2
INT_SAUSA300_0927_comK	0	15	15
INT_srn_9340_sRNA287_SAUSA300_1772	0	7	7
INT_mnhA_SAUSA300_0856	0	1	1
INT_srn_1060_Teg149_srn_1070_Sau41	0	1	1
INT_atpG_atpG	0	2	2
INT_SAUSA300_1658_tpx	0	1	1
INT_srn_1070_Sau41_srn_1080_RsaX05	0	6	6
INT_SAUSA300_0979_srn_2330_Sau11	0	1	1
INT_SAUSA300_2018_SAUSA300_2019	0	4	4
INT_rrfD_rrlD	0	10	10
INT_pstS_srn_2940_sRNA233	0	1	1
INT_SAUSA300_0029_SAUSA300_0030	0	1	1
INT_SAUSA300_0692_SAUSA300_0693	0	1	1
INT_rocF_srn_9490_sRNA337	0	20	20
INT_SAUSA300_0953_SAUSA300_0954	0	1	1
INT_gpmA_SAUSA300_2363	0	1	1
INT_rpoA_rpsK	0	1	1
INT_srn_1500_Sau6667_srn_1505_S204	0	2	2
INT_rrsE_srn_4160_Sau25	0	5	5
INT_srn_2740_Teg108_SAUSA300_1205	0	6	6
INT_SAUSA300_1923_SAUSA300_1924	0	1	1
INT_secF_yajC	0	1	1
INT_SAUSA300_2404_SAUSA300_2405	0	1	1
INT_srn_1490_Sau6477_SAUSA300_0559	0	1	1
INT_rpiA_SAUSA300_2284	0	1	1
INT_srn_4390_rsaOG_SAUSA300_2261	0	1	1
INT_SAUSA300_1101_gmk	0	1	1
INT_SAUSA300_2471_SAUSA300_2472	0	1	1
INT_SAUSA300_0390_srn_0950_Sau63	0	1	1
INT_cmk_cmk	0	1	1
INT_rpmG_pbp3	0	2	2
INT_secF_secF	0	3	3
INT_SAUSA300_1916_SAUSA300_1918	0	2	2
INT_hemE_SAUSA300_1784	0	1	1
INT_SAUSA300_1697_SAUSA300_1698	0	1	1
INT_SAUSA300_0848_mnhG	0	1	1
INT_srn_4160_Sau25_SAUSA300_2125	0	1	1
INT_ctpA_SAUSA300_1314	0	1	1
INT_SAUSA300_1796_SAUSA300_1797	0	1	1
INT_rumA_SAUSA300_1879	0	1	1
INT_SAUSA300_1637_srn_3340_Teg72	0	1	1
INT_sdrH_SAUSA300_1986	0	1	1
INT_SAUSA300_1653_SAUSA300_1654	0	1	1
INT_srn_2490_sRNA206_SAUSA300_1059	0	2	2
INT_engA_rpsA	0	1	1
INT_SAUSA300_0561_srn_1500_Sau6667	0	1	1
INT_SAUSA300_2642_SAUSA300_2643	0	2	2
INT_SAUSA300_1847_SAUSA300_1848	0	1	1

## misc_RNA	123	0
ssrA	123	0	123
