The following contents displays predicted prophage regions
first line of each prophage describes the prophage information and the following lines describe the proteins and homology proteins in uniprot database
bacteria_id bac_def genome_size prophage_start  prophage_end    key_proteins    best_hit_species    CDS_number  attl_region attr_region
>prophage 1
NZ_CP029152	Clostridioides difficile strain CDT4 chromosome, complete genome	4240954	273722	280426	4240954		Synechococcus_phage(42.86%)	7	NA	NA
WP_003425291.1|273722_274235_-	nitroreductase family protein	NA	A0A1V0E011	Clostridioides_phage	87.6	7.8e-84
WP_003425290.1|274684_275161_+	5-(carboxyamino)imidazole ribonucleotide mutase	NA	A0A2P0VNU7	Tetraselmis_virus	45.8	6.9e-26
WP_003420966.1|275166_275865_+	phosphoribosylaminoimidazolesuccinocarboxamide synthase	NA	A0A0E3F9V5	Synechococcus_phage	43.9	1.5e-45
WP_003425288.1|275876_277244_+	amidophosphoribosyltransferase	NA	A0A0M3SGR2	Mollivirus	31.0	2.6e-49
WP_003425286.1|277237_278314_+	phosphoribosylformylglycinamidine cyclo-ligase	NA	R9TMC7	Synechococcus_phage	42.2	1.7e-64
WP_003425284.1|278307_278901_+	phosphoribosylglycinamide formyltransferase	NA	M4QRX9	Synechococcus_phage	40.4	5.6e-25
WP_003420974.1|278893_280426_+	bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase	NA	E3SNU8	Prochlorococcus_phage	49.7	2.3e-38
>prophage 2
NZ_CP029152	Clostridioides difficile strain CDT4 chromosome, complete genome	4240954	397205	415683	4240954	integrase	Streptococcus_phage(100.0%)	20	393707:393724	415695:415712
393707:393724	attL	AATTTACTACTTATTTAC	NA	NA	NA	NA
WP_008792581.1|397205_397532_+	YdcP family protein	NA	A0A1S5SF38	Streptococcus_phage	53.4	1.1e-25
WP_008687119.1|397547_397931_+	YdcP family protein	NA	A0A1S5SF96	Streptococcus_phage	55.9	8.9e-32
WP_008687118.1|398032_398797_+	MBL fold metallo-hydrolase	NA	NA	NA	NA	NA
WP_044593066.1|398895_400290_+	cell division protein FtsK	NA	A0A1S5SFB5	Streptococcus_phage	65.7	4.8e-176
WP_000398284.1|400467_401673_+	XRE family transcriptional regulator	NA	A0A1S5SEX3	Streptococcus_phage	100.0	2.8e-233
WP_001009056.1|401715_401937_+	hypothetical protein	NA	A0A1S5SEY0	Streptococcus_phage	100.0	4.3e-31
WP_000342539.1|402053_402551_+	antirestriction protein ArdA	NA	A0A1S5SF25	Streptococcus_phage	100.0	1.7e-91
WP_000506270.1|402525_403032_+	conjugal transfer protein	NA	A0A1S5SEX7	Streptococcus_phage	100.0	8.6e-91
WP_000331160.1|403015_405463_+	ATP-binding protein	NA	A0A1S5SF64	Streptococcus_phage	100.0	0.0e+00
WP_000804748.1|405465_407643_+	membrane protein	NA	A0A1S5SF30	Streptococcus_phage	100.0	0.0e+00
WP_000769868.1|407639_408641_+	peptidase P60	NA	A0A1S5SEZ8	Streptococcus_phage	100.0	5.0e-191
WP_001224320.1|408637_409573_+	conjugal transfer protein	NA	A0A1S5SF22	Streptococcus_phage	99.0	7.7e-170
WP_001814923.1|409815_409932_+	tetracycline resistance determinant leader peptide	NA	NA	NA	NA	NA
WP_000691736.1|409947_411867_+	tetracycline resistance ribosomal protection protein Tet(M)	NA	A0A1S5SF82	Streptococcus_phage	99.5	0.0e+00
WP_000336323.1|411985_412153_+	conjugal transfer protein	NA	D0R0F6	Streptococcus_phage	68.0	1.6e-14
WP_001227347.1|412212_412566_-	helix-turn-helix transcriptional regulator	NA	A0A1S5SFA6	Streptococcus_phage	100.0	1.3e-58
WP_000804885.1|413070_413493_+	sigma-70 family RNA polymerase sigma factor	NA	A0A1S5SEW0	Streptococcus_phage	100.0	2.5e-72
WP_000857133.1|413489_413720_+	helix-turn-helix domain-containing protein	NA	A0A1S5SEX1	Streptococcus_phage	100.0	2.7e-36
WP_000814511.1|414180_414384_+	excisionase	NA	A0A1S5SF07	Streptococcus_phage	100.0	4.0e-31
WP_001291561.1|414465_415683_+|integrase	tyrosine-type recombinase/integrase	integrase	A0A1S5SEW7	Streptococcus_phage	100.0	3.7e-233
415695:415712	attR	AATTTACTACTTATTTAC	NA	NA	NA	NA
>prophage 3
NZ_CP029152	Clostridioides difficile strain CDT4 chromosome, complete genome	4240954	491032	497981	4240954		Streptococcus_phage(33.33%)	10	NA	NA
WP_079394419.1|491032_491863_+	replication initiator protein A	NA	Q708R2	Streptococcus_phage	38.2	9.0e-05
WP_002571012.1|491859_492702_+	ATP-binding protein	NA	H7BWC4	unidentified_phage	48.1	8.7e-64
WP_002571011.1|492716_492905_+	hypothetical protein	NA	NA	NA	NA	NA
WP_002571010.1|493016_494636_+	recombinase family protein	NA	C7F8K5	Bacillus_phage	28.1	4.0e-25
WP_103900329.1|494897_495122_+	helix-turn-helix transcriptional regulator	NA	A0A2K5B263	Erysipelothrix_phage	38.2	2.8e-09
WP_108817224.1|495153_495678_+	hypothetical protein	NA	NA	NA	NA	NA
WP_108817245.1|495778_495910_+	hypothetical protein	NA	NA	NA	NA	NA
WP_131765963.1|495906_496719_+	hypothetical protein	NA	NA	NA	NA	NA
WP_103900326.1|496733_497126_+	hypothetical protein	NA	M1PLC5	Streptococcus_phage	45.5	5.2e-19
WP_108817225.1|497159_497981_-	helix-turn-helix transcriptional regulator	NA	A0A2R2ZGW9	Clostridioides_phage	39.8	1.2e-06
>prophage 4
NZ_CP029152	Clostridioides difficile strain CDT4 chromosome, complete genome	4240954	1496217	1568776	4240954	protease,tRNA,plate,portal,integrase,tail	Clostridium_phage(44.44%)	69	1495770:1495788	1570253:1570271
1495770:1495788	attL	TGAAATGGCAAAAAATTTA	NA	NA	NA	NA
WP_003428232.1|1496217_1497123_+|tRNA	tRNA pseudouridine(55) synthase TruB	tRNA	NA	NA	NA	NA
WP_003428231.1|1497253_1498183_+	bifunctional riboflavin kinase/FAD synthetase	NA	NA	NA	NA	NA
WP_003419491.1|1498286_1498544_+	30S ribosomal protein S15	NA	NA	NA	NA	NA
WP_021387801.1|1498783_1499635_+	DegV family protein	NA	NA	NA	NA	NA
WP_003428229.1|1499759_1501871_+	polyribonucleotide nucleotidyltransferase	NA	NA	NA	NA	NA
WP_003428228.1|1502136_1502880_+	polysaccharide deacetylase family protein	NA	NA	NA	NA	NA
WP_003428227.1|1503037_1504285_+	insulinase family protein	NA	G3MBJ8	Bacillus_virus	34.9	6.6e-52
WP_003419503.1|1504319_1504565_+	YlmC/YmxH family sporulation protein	NA	NA	NA	NA	NA
WP_003428226.1|1504574_1505798_+	aspartate kinase	NA	NA	NA	NA	NA
WP_003433325.1|1505910_1506645_+|protease	Clp protease	protease	NA	NA	NA	NA
WP_003428223.1|1506767_1509182_+	DNA translocase FtsK	NA	A0A218M9A2	Mycobacterium_phage	50.4	3.3e-92
WP_003428222.1|1509184_1510243_+|tRNA	tRNA 2-selenouridine(34) synthase MnmH	tRNA	NA	NA	NA	NA
WP_003428221.1|1510236_1511571_+	30S ribosomal protein S12 methylthiotransferase RimO	NA	NA	NA	NA	NA
WP_021387802.1|1511557_1512100_+	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase	NA	NA	NA	NA	NA
WP_003428218.1|1512387_1513434_+	recombinase RecA	NA	A0A0S2MVG1	Bacillus_phage	63.5	2.7e-123
WP_003428216.1|1513609_1515151_+	ribonuclease Y	NA	NA	NA	NA	NA
WP_003428215.1|1515785_1517567_+	UvrD-helicase domain-containing protein	NA	NA	NA	NA	NA
WP_003428214.1|1517648_1518197_-	signal peptidase I	NA	NA	NA	NA	NA
WP_009905410.1|1518218_1519043_-	undecaprenyl-diphosphate phosphatase	NA	NA	NA	NA	NA
WP_009889110.1|1519299_1520208_+|integrase	tyrosine-type recombinase/integrase	integrase	NA	NA	NA	NA
WP_021387804.1|1520351_1521797_+	adenylosuccinate lyase	NA	NA	NA	NA	NA
WP_003428210.1|1522107_1522560_+	MarR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003428209.1|1522963_1524541_+	PTS transporter subunit EIIC	NA	NA	NA	NA	NA
WP_003428208.1|1524688_1525441_+	MurR/RpiR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003428207.1|1525579_1526941_+	6-phospho-alpha-glucosidase	NA	NA	NA	NA	NA
WP_003428206.1|1527031_1528228_-	pyridoxal phosphate-dependent aminotransferase	NA	NA	NA	NA	NA
WP_003428205.1|1528612_1529563_+	galactose-1-phosphate uridylyltransferase	NA	NA	NA	NA	NA
WP_003428204.1|1529715_1530468_+	exodeoxyribonuclease III	NA	E3T4M6	Cafeteria_roenbergensis_virus	44.8	3.2e-57
WP_003428203.1|1530559_1531336_-	exonuclease domain-containing protein	NA	NA	NA	NA	NA
WP_003428202.1|1531650_1533549_+	glutamine synthetase	NA	NA	NA	NA	NA
WP_003428201.1|1533676_1534798_-	galactosyldiacylglycerol synthase	NA	NA	NA	NA	NA
WP_009889116.1|1534996_1535329_+	PadR family transcriptional regulator	NA	NA	NA	NA	NA
WP_003428198.1|1535315_1536374_+	DUF1700 domain-containing protein	NA	NA	NA	NA	NA
WP_003428197.1|1536366_1537437_+	DUF4097 family beta strand repeat protein	NA	NA	NA	NA	NA
WP_003428196.1|1537538_1538075_+	lipoprotein	NA	NA	NA	NA	NA
WP_021393263.1|1538190_1538898_+	lantibiotic protection ABC transporter ATP-binding protein	NA	A0A2H4PQG7	Staphylococcus_phage	48.5	9.6e-56
WP_003428194.1|1538899_1539616_+	lantibiotic immunity ABC transporter MutE/EpiE family permease subunit	NA	NA	NA	NA	NA
WP_021427419.1|1539617_1540376_+	lantibiotic immunity ABC transporter MutG family permease subunit	NA	NA	NA	NA	NA
WP_021387809.1|1540510_1541899_+	two-component system sensor histidine kinase	NA	NA	NA	NA	NA
WP_003428191.1|1541974_1542796_-	pyridoxamine kinase	NA	NA	NA	NA	NA
WP_021427410.1|1543046_1544201_+	amidase domain-containing protein	NA	NA	NA	NA	NA
WP_003419624.1|1544383_1544584_+	cold-shock protein	NA	A0A1W6JNX5	Morganella_phage	66.2	2.7e-16
WP_009889129.1|1545004_1545433_+	CBS domain-containing protein	NA	NA	NA	NA	NA
WP_021387811.1|1545575_1546331_-	PPIC-type PPIASE domain protein	NA	NA	NA	NA	NA
WP_003428188.1|1546451_1546868_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003428186.1|1547031_1547538_-	hypothetical protein	NA	A0A0A8WEK1	Clostridium_phage	67.1	4.0e-56
WP_003428185.1|1547619_1547940_-	XRE family transcriptional regulator	NA	A0A0A8WE28	Clostridium_phage	54.5	3.7e-23
WP_003419641.1|1548108_1548306_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_003428183.1|1548410_1548851_+	hypothetical protein	NA	A0A090EUN5	Clostridium_phage	51.4	6.0e-32
WP_003428180.1|1549099_1549543_+	hypothetical protein	NA	A0A1V0DZX9	Clostridioides_phage	36.7	2.0e-19
WP_003428178.1|1549547_1550612_+|portal	phage portal protein	portal	A0A1V0DZX4	Clostridioides_phage	53.1	1.2e-97
WP_003419646.1|1550625_1551054_+|tail	phage tail tube protein	tail	A0A1V0DZX1	Clostridioides_phage	51.8	2.8e-34
WP_003428176.1|1551167_1551614_+|portal	phage portal protein	portal	A0A0A7RTP2	Clostridium_phage	36.4	1.8e-12
WP_003428170.1|1551807_1554207_+	hypothetical protein	NA	A0A1V0DZX3	Clostridioides_phage	45.6	6.4e-19
WP_003428168.1|1554206_1554629_+	hypothetical protein	NA	A0A090DBR9	Clostridium_phage	71.1	1.7e-52
WP_003428166.1|1554910_1556443_+	cell wall XkdQ hydrolase	NA	A0A1V0DZX6	Clostridioides_phage	79.7	1.8e-237
WP_003428163.1|1556458_1556785_+	DUF2577 domain-containing protein	NA	J9QE86	Clostridium_phage	94.4	2.3e-52
WP_003428161.1|1556784_1557213_+	DUF2634 domain-containing protein	NA	A0A0A8WJ32	Clostridium_phage	82.4	5.8e-64
WP_003428158.1|1557205_1558258_+|plate	baseplate J/gp47 family protein	plate	A0A0A8WFP3	Clostridium_phage	69.8	5.7e-137
WP_003428156.1|1558254_1558953_+	DUF2313 domain-containing protein	NA	A0A090D815	Clostridium_phage	56.9	5.5e-48
WP_003428154.1|1558953_1559940_+|tail	phage tail protein	tail	A0A2H4J039	uncultured_Caudovirales_phage	46.8	7.6e-59
WP_003428152.1|1559961_1565193_+	chromosome condensation regulator	NA	A0A0A8WEY5	Clostridium_phage	31.3	3.4e-81
WP_003428149.1|1565209_1565563_+	hypothetical protein	NA	A0A0A8WJF2	Clostridium_phage	42.1	5.5e-12
WP_003419670.1|1565825_1566086_+	hypothetical protein	NA	E2ELK7	Clostridium_phage	90.6	9.9e-35
WP_003419674.1|1566309_1566765_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003428147.1|1566992_1567412_-	helix-turn-helix domain-containing protein	NA	S5MUV6	Brevibacillus_phage	37.2	5.4e-06
WP_003428146.1|1567710_1567920_+	helix-turn-helix transcriptional regulator	NA	Q5YAA3	Bacillus_phage	47.2	5.9e-06
WP_009889160.1|1567951_1568161_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003428144.1|1568377_1568776_-	helix-turn-helix domain-containing protein	NA	A0A1L2JY18	Aeribacillus_phage	29.7	2.7e-07
1570253:1570271	attR	TAAATTTTTTGCCATTTCA	NA	NA	NA	NA
>prophage 5
NZ_CP029152	Clostridioides difficile strain CDT4 chromosome, complete genome	4240954	1650185	1659914	4240954		Pandoravirus(37.5%)	11	NA	NA
WP_003429412.1|1650185_1650770_+	aminodeoxychorismate/anthranilate synthase component II	NA	A0A0P0IKJ1	Acinetobacter_phage	53.7	1.7e-58
WP_003429413.1|1650771_1652121_+	aminodeoxychorismate synthase component I	NA	S4VNU7	Pandoravirus	41.2	2.9e-37
WP_003429414.1|1652110_1652854_+	aminodeoxychorismate lyase	NA	NA	NA	NA	NA
WP_003429415.1|1652887_1653589_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003429416.1|1653614_1654187_+	GTP cyclohydrolase I FolE	NA	E7DN69	Pneumococcus_phage	51.6	3.0e-44
WP_003429417.1|1654252_1655044_+	dihydropteroate synthase	NA	A0A0B5J4J5	Pandoravirus	30.0	9.8e-25
WP_009889257.1|1655054_1655420_+	dihydroneopterin aldolase	NA	NA	NA	NA	NA
WP_003429419.1|1655412_1655919_+	2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinase	NA	S4VNV0	Pandoravirus	36.6	2.5e-13
WP_003429421.1|1655899_1656685_+	3-deoxy-7-phosphoheptulonate synthase	NA	E3T537	Cafeteria_roenbergensis_virus	28.3	1.0e-13
WP_009896376.1|1656939_1658730_+	DNA primase	NA	A0A0K1LMQ9	Caulobacter_phage	32.6	1.2e-51
WP_003429425.1|1658747_1659914_+	RNA polymerase sigma factor RpoD	NA	M4SMP8	Cyanophage	36.8	9.6e-37
>prophage 6
NZ_CP029152	Clostridioides difficile strain CDT4 chromosome, complete genome	4240954	1785561	1841153	4240954	plate,terminase,portal,integrase,tail,capsid	Clostridium_phage(82.35%)	59	1787396:1787423	1842502:1842529
WP_003429802.1|1785561_1787250_+	biosynthetic-type acetolactate synthase large subunit	NA	A0A0P0YLY7	Yellowstone_lake_phycodnavirus	29.2	6.4e-50
1787396:1787423	attL	TAGAATAATATTACAACTTAAGTAAATA	NA	NA	NA	NA
WP_003433492.1|1787607_1788738_-|integrase	site-specific integrase	integrase	A0A0A8WIE1	Clostridium_phage	99.5	5.0e-216
WP_003429804.1|1788977_1789484_-	ImmA/IrrE family metallo-endopeptidase	NA	A0A0A8WEK1	Clostridium_phage	100.0	1.5e-87
WP_003429805.1|1789746_1791336_-	hypothetical protein	NA	A0A1S5SA14	Streptococcus_phage	27.9	4.0e-33
WP_003433494.1|1791359_1791905_-	XRE family transcriptional regulator	NA	A0A0A8WJ60	Clostridium_phage	53.3	2.6e-45
WP_003433496.1|1792085_1792301_+	helix-turn-helix transcriptional regulator	NA	A0A0A8WIG0	Clostridium_phage	77.5	3.8e-24
WP_003433498.1|1792331_1793105_+	Rha family transcriptional regulator	NA	A0A0A8WIJ5	Clostridium_phage	39.6	4.6e-35
WP_021387707.1|1793224_1794055_+	phage antirepressor KilAC domain-containing protein	NA	A0A0A8WIE3	Clostridium_phage	62.8	4.4e-84
WP_009888812.1|1794101_1794311_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003433505.1|1794320_1794695_-	hypothetical protein	NA	A0A1L5C299	Pseudoalteromonas_phage	37.1	2.2e-11
WP_003433507.1|1794770_1794968_+	helix-turn-helix transcriptional regulator	NA	A0A0A8WE47	Clostridium_phage	92.3	4.9e-26
WP_003433509.1|1794998_1795391_+	helix-turn-helix domain-containing protein	NA	A0A0A8WHS2	Clostridium_phage	94.6	6.7e-59
WP_003433513.1|1795591_1796029_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003433514.1|1796040_1797207_+	DUF2800 domain-containing protein	NA	S5MUB5	Brevibacillus_phage	55.9	1.1e-117
WP_003433515.1|1797221_1797557_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003429822.1|1797609_1798182_+	DNA-directed RNA polymerase sigma-70 factor	NA	NA	NA	NA	NA
WP_003433516.1|1798204_1798777_+	DUF2815 family protein	NA	S5MC21	Brevibacillus_phage	66.7	8.5e-63
WP_003433517.1|1798776_1800735_+	DNA polymerase	NA	A0A0A7RTL3	Clostridium_phage	69.4	5.4e-266
WP_003433519.1|1800746_1803164_+	virulence-associated protein E	NA	A0A0A7RTG3	Clostridium_phage	67.7	0.0e+00
WP_003433522.1|1803445_1803772_+	VRR-NUC domain-containing protein	NA	A0A2K5B272	Erysipelothrix_phage	55.4	8.7e-20
WP_003433524.1|1803720_1805091_+	DEAD/DEAH box helicase	NA	A0A1S7FYY5	Listeria_phage	60.3	8.4e-157
WP_003433526.1|1805244_1805724_+	hypothetical protein	NA	I2E8Y5	Clostridium_phage	51.6	3.3e-36
WP_003429832.1|1806208_1806445_+	hypothetical protein	NA	A0A0A8WJQ8	Clostridium_phage	96.2	3.3e-37
WP_003429833.1|1806747_1807722_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003429834.1|1807742_1808252_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003433528.1|1808322_1809015_+	hypothetical protein	NA	A0A0A8WFS6	Clostridium_phage	98.3	1.7e-121
WP_003433530.1|1808992_1810246_+|terminase	PBSX family phage terminase large subunit	terminase	X5JAB3	Clostridium_phage	99.0	3.0e-246
WP_003429837.1|1810251_1811691_+|portal	phage portal protein	portal	A0A0A8WFC0	Clostridium_phage	99.8	5.3e-279
WP_003429838.1|1811680_1813174_+|capsid	minor capsid protein	capsid	X5JAI9	Clostridium_phage	96.8	1.1e-284
WP_009901430.1|1813139_1813382_+	hypothetical protein	NA	X5JAV8	Clostridium_phage	100.0	3.4e-37
WP_003433534.1|1813691_1814255_+	scaffold protein	NA	X5JAB4	Clostridium_phage	89.3	3.0e-84
WP_003429841.1|1814266_1815166_+|capsid	phage capsid protein	capsid	A0A0A8WFI8	Clostridium_phage	100.0	2.8e-169
WP_003433536.1|1815165_1815399_+	hypothetical protein	NA	A0A0A8WFD0	Clostridium_phage	96.1	3.2e-32
WP_009888836.1|1815408_1815810_+	hypothetical protein	NA	X5JAJ0	Clostridium_phage	97.0	8.1e-68
WP_003433540.1|1815803_1816151_+	hypothetical protein	NA	X5JAV9	Clostridium_phage	99.1	1.1e-57
WP_003433542.1|1816150_1816576_+	HK97 gp10 family phage protein	NA	A0A0A8WFV8	Clostridium_phage	97.9	3.2e-75
WP_003433544.1|1816568_1817006_+	hypothetical protein	NA	X5JAB5	Clostridium_phage	92.4	2.8e-74
WP_003433550.1|1817175_1818486_+	hypothetical protein	NA	X5JAJ1	Clostridium_phage	94.0	7.3e-235
WP_003429851.1|1818502_1818973_+|tail	phage tail tube protein	tail	A0A0A8WJ62	Clostridium_phage	82.1	7.0e-71
WP_003429853.1|1819044_1819485_+|portal	phage portal protein	portal	X5JAB6	Clostridium_phage	63.7	8.6e-47
WP_021387708.1|1821134_1821887_+	SHOCT domain-containing protein	NA	A0A090DCP8	Clostridium_phage	51.6	6.2e-61
WP_003433557.1|1822190_1822364_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003433559.1|1822487_1823315_+	hypothetical protein	NA	X5JAW1	Clostridium_phage	66.3	5.2e-85
WP_003433565.1|1823952_1824531_+	hypothetical protein	NA	A0A0A8WFW4	Clostridium_phage	90.3	3.8e-87
WP_003433567.1|1824606_1826973_+	tape measure protein	NA	A0A0A8WJT6	Clostridium_phage	71.3	1.3e-282
WP_003433569.1|1826988_1827690_+	LysM peptidoglycan-binding domain-containing protein	NA	A0A0A8WFE5	Clostridium_phage	93.5	8.4e-121
WP_003433571.1|1827682_1829647_+	cell wall hydrolase	NA	A0A0A8WIF2	Clostridium_phage	86.1	6.1e-310
WP_003433573.1|1829660_1829921_+	DUF2577 domain-containing protein	NA	A0A0A8WJ65	Clostridium_phage	96.5	2.5e-38
WP_003433575.1|1829925_1830345_+	DUF2634 domain-containing protein	NA	A0A0A8WJV8	Clostridium_phage	98.6	3.9e-73
WP_032512186.1|1830345_1831392_+|plate	baseplate J/gp47 family protein	plate	X5JAB8	Clostridium_phage	94.2	2.6e-182
WP_003433579.1|1831384_1832002_+	YmfQ family protein	NA	A0A0A8WII4	Clostridium_phage	98.0	8.8e-114
WP_021363498.1|1832013_1833006_+|tail	phage tail protein	tail	A3QSB7	Clostridium_virus	94.1	1.5e-160
WP_003429875.1|1834755_1835103_+	hypothetical protein	NA	A3QSB8	Clostridium_virus	100.0	5.5e-57
WP_021363499.1|1835315_1835882_+	hypothetical protein	NA	A0A0A8WFF2	Clostridium_phage	78.7	1.2e-37
WP_021363500.1|1835912_1836203_+	hypothetical protein	NA	A0A0A8WIF5	Clostridium_phage	100.0	6.3e-46
WP_021363501.1|1836206_1836464_+	membrane protein	NA	A0A0A8WF70	Clostridium_phage	95.3	6.6e-39
WP_021387710.1|1837665_1838478_+	N-acetylmuramoyl-L-alanine amidase	NA	A0A0K2SUC5	Clostridium_phage	94.4	1.3e-149
WP_021388366.1|1838634_1840926_+	cell wall-binding repeat-containing protein	NA	NA	NA	NA	NA
WP_003433687.1|1840967_1841153_-	hypothetical protein	NA	A0A0A8WHQ4	Clostridium_phage	62.1	7.6e-13
1842502:1842529	attR	TAGAATAATATTACAACTTAAGTAAATA	NA	NA	NA	NA
>prophage 7
NZ_CP029152	Clostridioides difficile strain CDT4 chromosome, complete genome	4240954	2625175	2639316	4240954	integrase	Clostridium_phage(71.43%)	17	2631493:2631509	2646210:2646226
WP_003430370.1|2625175_2625922_-	N-acetylmuramoyl-L-alanine amidase	NA	A0A0A8WHU0	Clostridium_phage	67.5	3.9e-84
WP_021388194.1|2625921_2626179_-	membrane protein	NA	A0A0A8WF70	Clostridium_phage	83.5	7.5e-35
WP_003430368.1|2626198_2626429_-	membrane protein	NA	A0A0A8WEZ7	Clostridium_phage	97.4	4.8e-33
WP_003430367.1|2626486_2628034_-	hypothetical protein	NA	B6SBV0	Clostridium_virus	75.7	7.2e-181
WP_003430365.1|2628168_2628351_-	hypothetical protein	NA	J9QDY8	Clostridium_phage	90.0	1.2e-23
WP_003430361.1|2628656_2630150_-	hypothetical protein	NA	J9QE87	Clostridium_phage	55.2	6.0e-108
WP_003430350.1|2630165_2630513_-	hypothetical protein	NA	J9QED3	Clostridium_phage	68.5	1.9e-20
WP_071599207.1|2630500_2631784_-	DUF2313 domain-containing protein	NA	A0A0A8WFK0	Clostridium_phage	81.3	5.7e-131
2631493:2631509	attL	CAGCAGTTTCAAGACCA	NA	NA	NA	NA
WP_003430347.1|2632159_2632594_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003430345.1|2632681_2634241_-	cell wall-binding repeat-containing protein	NA	A0A2R2ZGK6	Clostridioides_phage	52.0	1.9e-72
WP_003430343.1|2634445_2634886_+	hypothetical protein	NA	A0A0A8WIE1	Clostridium_phage	69.8	1.9e-54
WP_021388401.1|2634912_2635587_+|integrase	site-specific integrase	integrase	A0A0A8WIE1	Clostridium_phage	54.7	4.1e-64
WP_003430677.1|2636554_2636932_-	hypothetical protein	NA	A0A0A8WJU1	Clostridium_phage	91.2	3.6e-54
WP_003430678.1|2637491_2637680_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003430679.1|2637840_2638191_+	DUF3796 domain-containing protein	NA	NA	NA	NA	NA
WP_003430680.1|2638192_2638393_+	helix-turn-helix transcriptional regulator	NA	A0A1V0E021	Clostridioides_phage	45.8	3.7e-05
WP_003423148.1|2639115_2639316_+	cold-shock protein	NA	A0A1X9IGI9	Lactococcus_phage	71.4	2.0e-19
2646210:2646226	attR	TGGTCTTGAAACTGCTG	NA	NA	NA	NA
>prophage 8
NZ_CP029152	Clostridioides difficile strain CDT4 chromosome, complete genome	4240954	2877650	2885419	4240954	holin	Clostridium_phage(57.14%)	8	NA	NA
WP_003431032.1|2877650_2878034_-	transcriptional regulator	NA	A0A090DCS9	Clostridium_phage	89.8	4.1e-61
WP_003431034.1|2878815_2879016_+	cold-shock protein	NA	A0A1X9IGI9	Lactococcus_phage	68.3	5.0e-18
WP_003431035.1|2879446_2880784_+	sensor histidine kinase	NA	X5JAC0	Clostridium_phage	59.9	1.3e-138
WP_003431036.1|2880826_2881408_+	accessory gene regulator B family protein	NA	X5JB40	Clostridium_phage	49.2	1.0e-42
WP_003431037.1|2881425_2881587_+	cyclic lactone autoinducer peptide	NA	NA	NA	NA	NA
WP_003431038.1|2881608_2882406_-	N-acetylmuramoyl-L-alanine amidase	NA	A0A0A8WE15	Clostridium_phage	90.7	1.1e-140
WP_003431039.1|2882402_2882663_-|holin	holin	holin	A3QSC5	Clostridium_virus	77.6	7.9e-32
WP_003431041.1|2884048_2885419_-	cell wall-binding protein Cwp29	NA	A0A2R2ZGK6	Clostridioides_phage	43.9	1.6e-70
>prophage 9
NZ_CP029152	Clostridioides difficile strain CDT4 chromosome, complete genome	4240954	3190739	3199692	4240954		Catovirus(50.0%)	8	NA	NA
WP_021388169.1|3190739_3192653_-	polysaccharide biosynthesis protein	NA	A0A1V0SAI8	Catovirus	29.8	1.1e-26
WP_003426494.1|3192736_3193828_-	glycosyltransferase	NA	A0A1V0SL50	Klosneuvirus	26.2	2.3e-16
WP_021388170.1|3193833_3195129_-	UDP-glucose/GDP-mannose dehydrogenase family protein	NA	A0A127AXI2	Bacillus_phage	43.4	4.9e-90
WP_003426498.1|3195154_3195907_-	glycosyltransferase family 2 protein	NA	A0A1V0SAH6	Catovirus	40.5	4.6e-16
WP_003426500.1|3195954_3196863_-	glycosyltransferase family 2 protein	NA	NA	NA	NA	NA
WP_003426502.1|3196884_3197634_-	glycosyltransferase family 2 protein	NA	A0A1V0SAH6	Catovirus	38.8	1.2e-16
WP_021359578.1|3197662_3198838_-	poly(glycerophosphate) glycerophosphotransferase	NA	NA	NA	NA	NA
WP_009897935.1|3198852_3199692_-	glycosyltransferase family 2 protein	NA	A0A2P1ELT8	Moumouvirus	26.3	7.0e-05
>prophage 10
NZ_CP029152	Clostridioides difficile strain CDT4 chromosome, complete genome	4240954	3641066	3677588	4240954	holin,protease,head,plate,portal,terminase,integrase,tail,capsid	Clostridium_phage(79.49%)	47	3665942:3665959	3686745:3686762
WP_003427603.1|3641066_3643094_-	SAM-dependent DNA methyltransferase	NA	A0A220A2U5	Liberibacter_phage	24.0	2.6e-21
WP_003427605.1|3643555_3644035_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003427607.1|3644063_3644876_-	N-acetylmuramoyl-L-alanine amidase	NA	X5JAJ5	Clostridium_phage	93.3	4.2e-148
WP_003432725.1|3644875_3645133_-|holin	holin	holin	A0A0K2SUI8	Clostridium_phage	91.8	2.0e-40
WP_003426807.1|3645152_3645383_-	membrane protein	NA	A0A0A8WJR7	Clostridium_phage	97.4	2.8e-33
WP_021387718.1|3645453_3645987_-	hypothetical protein	NA	A0A0A8WFF2	Clostridium_phage	83.8	1.7e-28
WP_003426811.1|3646020_3646203_-	hypothetical protein	NA	J9QE73	Clostridium_phage	95.0	7.2e-24
WP_021387717.1|3646202_3646496_-	hypothetical protein	NA	J9QE35	Clostridium_phage	91.8	2.7e-44
WP_021387716.1|3646509_3648207_-	glycine rich family protein	NA	A0A090EUF1	Clostridium_phage	59.9	1.7e-135
WP_021387715.1|3648223_3649225_-|tail	phage tail protein	tail	A0A1V0DZY8	Clostridioides_phage	80.5	6.4e-114
WP_021387714.1|3649226_3649844_-	DUF2313 domain-containing protein	NA	J9QD29	Clostridium_phage	87.8	6.5e-101
WP_003429314.1|3649840_3650896_-|plate	baseplate J/gp47 family protein	plate	A0A0A8WFP3	Clostridium_phage	94.3	1.9e-185
WP_003429312.1|3650888_3651317_-	DUF2634 domain-containing protein	NA	J9QE34	Clostridium_phage	93.7	2.0e-72
WP_003432633.1|3651316_3651643_-	DUF2577 family protein	NA	J9QE86	Clostridium_phage	90.7	1.2e-48
WP_003429626.1|3651658_3653176_-	cell wall XkdQ hydrolase	NA	A0A0K2SUC1	Clostridium_phage	88.6	1.3e-254
WP_003429625.1|3653415_3654051_-	LysM peptidoglycan-binding domain-containing protein	NA	J9QDY6	Clostridium_phage	97.6	1.6e-118
WP_003429624.1|3654050_3655805_-	hypothetical protein	NA	A0A0K2SUF9	Clostridium_phage	92.3	2.4e-225
WP_003429622.1|3655988_3656372_-	hypothetical protein	NA	J9QED1	Clostridium_phage	100.0	6.8e-56
WP_003429621.1|3656420_3656870_-|tail	phage tail tube protein	tail	A0A0A8WF55	Clostridium_phage	93.3	1.4e-76
WP_003429620.1|3656882_3657950_-	hypothetical protein	NA	J9QDY5	Clostridium_phage	95.8	4.6e-187
WP_003429619.1|3657964_3658381_-	hypothetical protein	NA	A0A0K2SUF6	Clostridium_phage	94.9	1.1e-64
WP_003429618.1|3658392_3658806_-	hypothetical protein	NA	A0A0K2SUA7	Clostridium_phage	94.2	2.2e-68
WP_003429617.1|3658798_3659137_-|head	phage head closure protein	head	A0A0A8WI51	Clostridium_phage	98.2	9.8e-59
WP_003429616.1|3659138_3659426_-|head,tail	phage gp6-like head-tail connector protein	head,tail	A0A0A8WF50	Clostridium_phage	95.8	3.2e-42
WP_003429615.1|3659435_3660704_-|capsid	phage major capsid protein	capsid	A0A0K2SUH4	Clostridium_phage	97.9	2.8e-231
WP_003429614.1|3660696_3661434_-|protease	Clp protease ClpP	protease	A0A0A8WFM9	Clostridium_phage	88.6	1.5e-123
WP_003429612.1|3661439_3662594_-|portal	phage portal protein	portal	J9QE83	Clostridium_phage	93.5	2.4e-205
WP_003429611.1|3662609_3664259_-|terminase	terminase large subunit	terminase	A0A0A8WI49	Clostridium_phage	94.9	0.0e+00
WP_003429610.1|3664255_3664645_-	hypothetical protein	NA	A0A090C9N7	Clostridium_phage	100.0	3.2e-61
WP_003429609.1|3664742_3665036_-	HNH endonuclease	NA	J9QDZ3	Clostridium_phage	91.8	5.2e-48
WP_003429608.1|3665028_3665322_-	hypothetical protein	NA	J9QE40	Clostridium_phage	48.9	8.3e-14
WP_003429607.1|3665518_3666118_-|integrase	tyrosine-type recombinase/integrase	integrase	A0A0A8WF93	Clostridium_phage	89.8	6.8e-79
3665942:3665959	attL	TCTTTTTAAAGCTTCTTT	NA	NA	NA	NA
WP_003429606.1|3666404_3667232_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003429605.1|3667603_3668116_-	hypothetical protein	NA	A0A1V0E028	Clostridioides_phage	45.2	3.6e-28
WP_003429602.1|3668301_3668595_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003429601.1|3668608_3668866_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003429600.1|3668855_3669485_-	sigma-70 family RNA polymerase sigma factor	NA	NA	NA	NA	NA
WP_003429599.1|3669499_3670834_-	helicase	NA	A0A222ZRG2	Mycobacterium_phage	28.2	7.2e-28
WP_003429598.1|3670848_3671613_-	hypothetical protein	NA	B4XYS6	Lactobacillus_phage	29.4	8.0e-24
WP_003429597.1|3671636_3671867_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_003429596.1|3671878_3672316_-	helix-turn-helix transcriptional regulator	NA	A0A1L2BY71	Clostridium_phage	38.2	1.3e-15
WP_003429595.1|3672343_3672562_-	helix-turn-helix domain-containing protein	NA	NA	NA	NA	NA
WP_003429594.1|3672726_3673074_+	helix-turn-helix transcriptional regulator	NA	A0A090D830	Clostridium_phage	34.8	1.0e-10
WP_003429593.1|3673120_3674281_-	endonuclease	NA	A0A1S5SAB0	Streptococcus_phage	54.1	3.2e-64
WP_003429591.1|3675034_3675256_+	helix-turn-helix transcriptional regulator	NA	NA	NA	NA	NA
WP_003429590.1|3675303_3676482_+|integrase	site-specific integrase	integrase	A0A1B0T6A8	Bacillus_phage	31.0	2.6e-37
WP_003421925.1|3677132_3677588_-	SsrA-binding protein SmpB	NA	W5RAM5	Staphylococcus_phage	54.5	2.6e-38
3686745:3686762	attR	TCTTTTTAAAGCTTCTTT	NA	NA	NA	NA
>prophage 1
NZ_CP029153	Clostridioides difficile strain CDT4 plasmid unnamed1, complete sequence	48594	409	11901	48594		Clostridium_phage(61.54%)	21	NA	NA
WP_003425640.1|409_946_-	LemA family protein	NA	A0A1X9IGG1	Lactococcus_phage	39.6	7.6e-29
WP_021427389.1|945_1272_-	hypothetical protein	NA	NA	NA	NA	NA
WP_022616540.1|1461_2046_-	sigma-70 family RNA polymerase sigma factor	NA	S5MNV1	Brevibacillus_phage	28.9	1.8e-07
WP_021427395.1|2023_2401_-	single-stranded DNA-binding protein	NA	E2ELN0	Clostridium_phage	57.0	1.1e-37
WP_021373851.1|2397_2580_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003431628.1|2636_3341_-	hypothetical protein	NA	A0A0A7RUC6	Clostridium_phage	57.1	2.2e-68
WP_003431627.1|3392_3779_-	hypothetical protein	NA	A0A0A7RUF3	Clostridium_phage	47.0	5.6e-18
WP_021427398.1|4149_5478_-	AAA family ATPase	NA	A0A2H4J8K1	uncultured_Caudovirales_phage	26.8	9.3e-20
WP_003425628.1|5499_5817_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003425627.1|5954_6143_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003425626.1|6135_6396_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003425625.1|6558_6771_+	hypothetical protein	NA	NA	NA	NA	NA
WP_003425624.1|6789_7008_-	hypothetical protein	NA	A0A090D836	Clostridium_phage	46.9	1.7e-08
WP_003425623.1|7034_7220_-	hypothetical protein	NA	NA	NA	NA	NA
WP_021427396.1|7247_7967_-	helix-turn-helix domain-containing protein	NA	A0A1V0E018	Clostridioides_phage	57.8	7.0e-30
WP_003425621.1|7995_8202_-	hypothetical protein	NA	E2ELM0	Clostridium_phage	49.3	2.7e-11
WP_003425619.1|8535_8910_+	helix-turn-helix transcriptional regulator	NA	A0A1V0E015	Clostridioides_phage	76.6	2.1e-46
WP_003425614.1|9543_9912_+	helix-turn-helix domain-containing protein	NA	E2ELL8	Clostridium_phage	82.6	8.5e-48
WP_009894554.1|9937_10093_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003425612.1|10679_11063_+	BlaI/MecI/CopY family transcriptional regulator	NA	A0A0A8WJP7	Clostridium_phage	45.7	5.6e-26
WP_003425609.1|11211_11901_-	HTH domain-containing protein	NA	E2ELL5	Clostridium_phage	41.7	1.7e-41
>prophage 2
NZ_CP029153	Clostridioides difficile strain CDT4 plasmid unnamed1, complete sequence	48594	17013	47876	48594	capsid,portal,integrase,plate,tail,holin	Clostridioides_phage(62.16%)	40	16825:16839	46227:46241
16825:16839	attL	ATAAAGAAAAAGCAA	NA	NA	NA	NA
WP_003428605.1|17013_17919_+	ParM/StbA family protein	NA	Q0SPH6	Clostridium_phage	28.6	5.2e-22
WP_021427390.1|18001_18517_+	hypothetical protein	NA	A0A0A8WEM4	Clostridium_phage	35.6	7.8e-23
WP_003428603.1|18527_18863_-	hypothetical protein	NA	A0A0A8WFI6	Clostridium_phage	45.0	3.7e-18
WP_003428602.1|19000_20107_-	DNA cytosine methyltransferase	NA	A0A0A8WIK9	Clostridium_phage	62.7	6.2e-126
WP_021427394.1|20178_20994_-	N-acetylmuramoyl-L-alanine amidase	NA	Q24LG3	Clostridium_phage	96.3	1.3e-149
WP_003432713.1|20993_21251_-|holin	holin	holin	A0A0K2SUI8	Clostridium_phage	96.5	5.4e-41
WP_021363500.1|21254_21545_-	hypothetical protein	NA	A0A0A8WIF5	Clostridium_phage	100.0	6.3e-46
WP_021393203.1|21575_22142_-	hypothetical protein	NA	A0A0A8WFF2	Clostridium_phage	81.1	8.5e-39
WP_003426796.1|22174_22357_-	hypothetical protein	NA	A0A090D845	Clostridium_phage	96.7	1.4e-24
WP_003426797.1|22356_22650_-	hypothetical protein	NA	A0A2R2ZGK0	Clostridioides_phage	75.3	6.6e-35
WP_044593088.1|24307_25309_-|tail	phage tail protein	tail	A0A090DCR2	Clostridium_phage	86.5	9.8e-139
WP_021427377.1|25309_25927_-	DUF2313 domain-containing protein	NA	J9QD29	Clostridium_phage	82.9	3.6e-91
WP_021427393.1|25928_26981_-|plate	baseplate J/gp47 family protein	plate	A0A1V0DZY2	Clostridioides_phage	90.3	4.7e-176
WP_009894588.1|26973_27408_-	DUF2634 domain-containing protein	NA	A0A1V0DZX2	Clostridioides_phage	90.1	6.5e-71
WP_003431637.1|27400_27733_-	DUF2577 family protein	NA	J9QE86	Clostridium_phage	87.0	3.1e-49
WP_021393679.1|27746_29264_-	nlpC/P60 family protein	NA	A0A1V0DZX6	Clostridioides_phage	88.0	6.7e-264
WP_021427397.1|29503_30139_-	LysM peptidoglycan-binding domain-containing protein	NA	A0A1V0DZX0	Clostridioides_phage	86.3	2.5e-108
WP_003425686.1|30196_30673_-	DUF4352 domain-containing protein	NA	NA	NA	NA	NA
WP_021427376.1|30719_34112_-|tail	phage tail tape measure protein	tail	A0A1V0DZX3	Clostridioides_phage	57.4	2.6e-175
WP_003425678.1|34291_34708_-|portal	phage portal protein	portal	A0A1V0DZX5	Clostridioides_phage	81.2	3.5e-58
WP_003425675.1|34723_35164_-|tail	phage tail tube protein	tail	A0A1V0DZX1	Clostridioides_phage	77.5	1.3e-63
WP_009894567.1|35179_36235_-|portal	phage portal protein	portal	A0A1V0DZX4	Clostridioides_phage	85.5	5.6e-169
WP_003425671.1|36235_36685_-	hypothetical protein	NA	A0A1V0DZX9	Clostridioides_phage	89.3	4.0e-68
WP_021427375.1|36693_37050_-	HK97 gp10 family phage protein	NA	A0A1V0DZV8	Clostridioides_phage	92.4	5.7e-57
WP_021427383.1|37049_37397_-	hypothetical protein	NA	A0A1V0DZW2	Clostridioides_phage	89.6	1.4e-55
WP_009894563.1|37408_37789_-	hypothetical protein	NA	A0A1V0DZU9	Clostridioides_phage	93.7	1.9e-58
WP_021427382.1|37772_38045_-	Rho termination factor	NA	A0A1V0DZV5	Clostridioides_phage	75.3	4.2e-28
WP_009894560.1|38058_38982_-	hypothetical protein	NA	A0A1V0DZW0	Clostridioides_phage	85.3	9.6e-149
WP_021402941.1|39010_39613_-	DUF4355 domain-containing protein	NA	A0A1V0DZW6	Clostridioides_phage	72.9	5.6e-73
WP_021427385.1|39638_39965_-	hypothetical protein	NA	A0A1J1J9Q7	Escherichia_phage	30.6	1.2e-05
WP_021427379.1|40024_40786_-|capsid	minor capsid protein	capsid	A0A1V0DZW9	Clostridioides_phage	87.0	7.8e-112
WP_021427387.1|40763_42041_-|portal	phage portal protein	portal	A0A1V0DZW8	Clostridioides_phage	87.3	1.7e-215
WP_022616541.1|42053_42257_-	hypothetical protein	NA	NA	NA	NA	NA
WP_021427391.1|42257_43997_-	hypothetical protein	NA	A0A1V0DZW7	Clostridioides_phage	93.3	0.0e+00
WP_003425650.1|44551_45010_-	helix-turn-helix domain-containing protein	NA	A0A1V0E032	Clostridioides_phage	77.6	3.9e-58
WP_021427388.1|45224_45869_-|integrase	tyrosine-type recombinase/integrase	integrase	A0A1V0E036	Clostridioides_phage	98.1	1.6e-113
WP_021368577.1|45872_46418_-	hypothetical protein	NA	A0A1V0E034	Clostridioides_phage	83.9	2.4e-75
46227:46241	attR	TTGCTTTTTCTTTAT	NA	NA	NA	NA
WP_003431634.1|46560_47004_-	hypothetical protein	NA	A0A1V0E028	Clostridioides_phage	72.4	9.3e-49
WP_009894535.1|47113_47371_-	hypothetical protein	NA	NA	NA	NA	NA
WP_003425645.1|47390_47876_-	hypothetical protein	NA	Q24LD1	Clostridium_phage	57.3	3.3e-15
