# macsyfinder 20230505.dev
# models : TFF-SF-0.0b2
# /home/bneron/Projects/GEM/MacSyFinder/MacSyFinder/py311/bin/macsyfinder --db-type gembase --models-dir tests/data/models/ --models TFF-SF all -w 5 --sequence-db tests/data/base/gembase_w_slow_genome.fa --timeout 2 --out-dir functional_test_timeout --index-dir .
#
# WARNING: The replicon 'THHY002.0321.00001.C001' has been SKIPPED. Cannot be solved before timeout.
#
# Systems found:

system id = PSAV001.0321.00001.C001_T4P_12
model = TFF-SF/T4P
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_00876', 'T4P_fimT', 816), ('PSAV001.0321.00001.C001_00877', 'T4P_fimT', 817), ('PSAV001.0321.00001.C001_00878', 'T4P_pilV', 818), ('PSAV001.0321.00001.C001_00879', 'T4P_pilW', 819), ('PSAV001.0321.00001.C001_00880', 'T4P_pilX', 820), ('PSAV001.0321.00001.C001_00881', 'T4P_pilY', 821), ('PSAV001.0321.00001.C001_00882', 'T4P_pilE', 822)], [('PSAV001.0321.00001.C001_01018', 'T4P_pilD', 926), ('PSAV001.0321.00001.C001_01019', 'T4P_pilC', 927), ('PSAV001.0321.00001.C001_01020', 'T4P_pilB', 928), ('PSAV001.0321.00001.C001_01021', 'T4P_pilA', 929)], [('PSAV001.0321.00001.C001_05037', 'MSH_mshM', 4719), ('PSAV001.0321.00001.C001_05040', 'T4P_pilQ', 4722), ('PSAV001.0321.00001.C001_05041', 'T4P_pilP', 4723), ('PSAV001.0321.00001.C001_05042', 'T4P_pilO', 4724), ('PSAV001.0321.00001.C001_05043', 'T4P_pilN', 4725), ('PSAV001.0321.00001.C001_05044', 'T4P_pilM', 4726)], [('PSAV001.0321.00001.C001_04959', 'T4P_pilT', 4643)]
occ = 1
wholeness = 0.944
loci nb = 3
score = 12.200

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [PSAV001.0321.00001.C001_T2SS_2])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 1 (T4P_pilX)
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 1 (MSH_mshM)

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_T4P_6
model = TFF-SF/T4P
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_00876', 'T4P_fimT', 816), ('PSAV001.0321.00001.C001_00877', 'T4P_fimT', 817), ('PSAV001.0321.00001.C001_00878', 'T4P_pilV', 818), ('PSAV001.0321.00001.C001_00879', 'T4P_pilW', 819), ('PSAV001.0321.00001.C001_00880', 'T4P_pilX', 820), ('PSAV001.0321.00001.C001_00881', 'T4P_pilY', 821), ('PSAV001.0321.00001.C001_00882', 'T4P_pilE', 822)], [('PSAV001.0321.00001.C001_01018', 'T4P_pilD', 926), ('PSAV001.0321.00001.C001_01019', 'T4P_pilC', 927), ('PSAV001.0321.00001.C001_01020', 'T4P_pilB', 928), ('PSAV001.0321.00001.C001_01021', 'T4P_pilA', 929)], [('PSAV001.0321.00001.C001_05037', 'MSH_mshM', 4719), ('PSAV001.0321.00001.C001_05040', 'T4P_pilQ', 4722), ('PSAV001.0321.00001.C001_05041', 'T4P_pilP', 4723), ('PSAV001.0321.00001.C001_05042', 'T4P_pilO', 4724), ('PSAV001.0321.00001.C001_05043', 'T4P_pilN', 4725), ('PSAV001.0321.00001.C001_05044', 'T4P_pilM', 4726)]
occ = 1
wholeness = 0.889
loci nb = 3
score = 11.500

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 0 ()
	- T4P_pilD: 1 (T4P_pilD [PSAV001.0321.00001.C001_T2SS_2])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 1 (T4P_pilX)
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 1 (MSH_mshM)

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_T4P_10
model = TFF-SF/T4P
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_00876', 'T4P_fimT', 816), ('PSAV001.0321.00001.C001_00877', 'T4P_fimT', 817), ('PSAV001.0321.00001.C001_00878', 'T4P_pilV', 818), ('PSAV001.0321.00001.C001_00879', 'T4P_pilW', 819), ('PSAV001.0321.00001.C001_00880', 'T4P_pilX', 820), ('PSAV001.0321.00001.C001_00881', 'T4P_pilY', 821), ('PSAV001.0321.00001.C001_00882', 'T4P_pilE', 822)], [('PSAV001.0321.00001.C001_05037', 'MSH_mshM', 4719), ('PSAV001.0321.00001.C001_05040', 'T4P_pilQ', 4722), ('PSAV001.0321.00001.C001_05041', 'T4P_pilP', 4723), ('PSAV001.0321.00001.C001_05042', 'T4P_pilO', 4724), ('PSAV001.0321.00001.C001_05043', 'T4P_pilN', 4725), ('PSAV001.0321.00001.C001_05044', 'T4P_pilM', 4726)], [('PSAV001.0321.00001.C001_04959', 'T4P_pilT', 4643)]
occ = 1
wholeness = 0.722
loci nb = 2
score = 8.700

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 0 ()
	- T4P_pilC: 0 ()
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 0 ()

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 1 (T4P_pilX)
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 1 (MSH_mshM)

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_T4P_4
model = TFF-SF/T4P
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_00876', 'T4P_fimT', 816), ('PSAV001.0321.00001.C001_00877', 'T4P_fimT', 817), ('PSAV001.0321.00001.C001_00878', 'T4P_pilV', 818), ('PSAV001.0321.00001.C001_00879', 'T4P_pilW', 819), ('PSAV001.0321.00001.C001_00880', 'T4P_pilX', 820), ('PSAV001.0321.00001.C001_00881', 'T4P_pilY', 821), ('PSAV001.0321.00001.C001_00882', 'T4P_pilE', 822)], [('PSAV001.0321.00001.C001_05037', 'MSH_mshM', 4719), ('PSAV001.0321.00001.C001_05040', 'T4P_pilQ', 4722), ('PSAV001.0321.00001.C001_05041', 'T4P_pilP', 4723), ('PSAV001.0321.00001.C001_05042', 'T4P_pilO', 4724), ('PSAV001.0321.00001.C001_05043', 'T4P_pilN', 4725), ('PSAV001.0321.00001.C001_05044', 'T4P_pilM', 4726)]
occ = 1
wholeness = 0.667
loci nb = 2
score = 8.000

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 0 ()
	- T4P_pilC: 0 ()
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 0 ()
	- T4P_pilD: 0 ()

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 1 (T4P_pilX)
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 1 (MSH_mshM)

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_T4P_9
model = TFF-SF/T4P
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_00876', 'T4P_fimT', 816), ('PSAV001.0321.00001.C001_00877', 'T4P_fimT', 817), ('PSAV001.0321.00001.C001_00878', 'T4P_pilV', 818), ('PSAV001.0321.00001.C001_00879', 'T4P_pilW', 819), ('PSAV001.0321.00001.C001_00880', 'T4P_pilX', 820), ('PSAV001.0321.00001.C001_00881', 'T4P_pilY', 821), ('PSAV001.0321.00001.C001_00882', 'T4P_pilE', 822)], [('PSAV001.0321.00001.C001_01018', 'T4P_pilD', 926), ('PSAV001.0321.00001.C001_01019', 'T4P_pilC', 927), ('PSAV001.0321.00001.C001_01020', 'T4P_pilB', 928), ('PSAV001.0321.00001.C001_01021', 'T4P_pilA', 929)], [('PSAV001.0321.00001.C001_04959', 'T4P_pilT', 4643)]
occ = 1
wholeness = 0.611
loci nb = 2
score = 7.700

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 0 ()
	- T4P_pilQ: 0 ()
	- T4P_pilN: 0 ()
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [PSAV001.0321.00001.C001_T2SS_2])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 1 (T4P_pilX)
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 0 ()
	- T4P_pilP: 0 ()
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_T4P_3
model = TFF-SF/T4P
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_00876', 'T4P_fimT', 816), ('PSAV001.0321.00001.C001_00877', 'T4P_fimT', 817), ('PSAV001.0321.00001.C001_00878', 'T4P_pilV', 818), ('PSAV001.0321.00001.C001_00879', 'T4P_pilW', 819), ('PSAV001.0321.00001.C001_00880', 'T4P_pilX', 820), ('PSAV001.0321.00001.C001_00881', 'T4P_pilY', 821), ('PSAV001.0321.00001.C001_00882', 'T4P_pilE', 822)], [('PSAV001.0321.00001.C001_01018', 'T4P_pilD', 926), ('PSAV001.0321.00001.C001_01019', 'T4P_pilC', 927), ('PSAV001.0321.00001.C001_01020', 'T4P_pilB', 928), ('PSAV001.0321.00001.C001_01021', 'T4P_pilA', 929)]
occ = 1
wholeness = 0.556
loci nb = 2
score = 7.000

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 0 ()
	- T4P_pilQ: 0 ()
	- T4P_pilN: 0 ()
	- T4P_pilT: 0 ()
	- T4P_pilD: 1 (T4P_pilD [PSAV001.0321.00001.C001_T2SS_2])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 1 (T4P_pilX)
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 0 ()
	- T4P_pilP: 0 ()
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_T4P_11
model = TFF-SF/T4P
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_01018', 'T4P_pilD', 926), ('PSAV001.0321.00001.C001_01019', 'T4P_pilC', 927), ('PSAV001.0321.00001.C001_01020', 'T4P_pilB', 928), ('PSAV001.0321.00001.C001_01021', 'T4P_pilA', 929)], [('PSAV001.0321.00001.C001_05037', 'MSH_mshM', 4719), ('PSAV001.0321.00001.C001_05040', 'T4P_pilQ', 4722), ('PSAV001.0321.00001.C001_05041', 'T4P_pilP', 4723), ('PSAV001.0321.00001.C001_05042', 'T4P_pilO', 4724), ('PSAV001.0321.00001.C001_05043', 'T4P_pilN', 4725), ('PSAV001.0321.00001.C001_05044', 'T4P_pilM', 4726)], [('PSAV001.0321.00001.C001_04959', 'T4P_pilT', 4643)]
occ = 1
wholeness = 0.611
loci nb = 2
score = 8.700

mandatory genes:
	- T4P_pilE: 0 ()
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [PSAV001.0321.00001.C001_T2SS_2])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 1 (MSH_mshM)

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_T4P_5
model = TFF-SF/T4P
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_01018', 'T4P_pilD', 926), ('PSAV001.0321.00001.C001_01019', 'T4P_pilC', 927), ('PSAV001.0321.00001.C001_01020', 'T4P_pilB', 928), ('PSAV001.0321.00001.C001_01021', 'T4P_pilA', 929)], [('PSAV001.0321.00001.C001_05037', 'MSH_mshM', 4719), ('PSAV001.0321.00001.C001_05040', 'T4P_pilQ', 4722), ('PSAV001.0321.00001.C001_05041', 'T4P_pilP', 4723), ('PSAV001.0321.00001.C001_05042', 'T4P_pilO', 4724), ('PSAV001.0321.00001.C001_05043', 'T4P_pilN', 4725), ('PSAV001.0321.00001.C001_05044', 'T4P_pilM', 4726)]
occ = 1
wholeness = 0.556
loci nb = 2
score = 8.000

mandatory genes:
	- T4P_pilE: 0 ()
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 0 ()
	- T4P_pilD: 1 (T4P_pilD [PSAV001.0321.00001.C001_T2SS_2])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 1 (MSH_mshM)

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_T4P_7
model = TFF-SF/T4P
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_01018', 'T4P_pilD', 926), ('PSAV001.0321.00001.C001_01019', 'T4P_pilC', 927), ('PSAV001.0321.00001.C001_01020', 'T4P_pilB', 928), ('PSAV001.0321.00001.C001_01021', 'T4P_pilA', 929)], [('PSAV001.0321.00001.C001_04959', 'T4P_pilT', 4643)]
occ = 1
wholeness = 0.278
loci nb = 1
score = 4.200

mandatory genes:
	- T4P_pilE: 0 ()
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 0 ()
	- T4P_pilQ: 0 ()
	- T4P_pilN: 0 ()
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [PSAV001.0321.00001.C001_T2SS_2])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 0 ()
	- T4P_pilP: 0 ()
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_T2SS_2
model = TFF-SF/T2SS
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_02322', 'T2SS_gspE', 2157), ('PSAV001.0321.00001.C001_02323', 'T2SS_gspF', 2158), ('PSAV001.0321.00001.C001_02324', 'T2SS_gspG', 2159), ('PSAV001.0321.00001.C001_02325', 'T2SS_gspH', 2160), ('PSAV001.0321.00001.C001_02326', 'T2SS_gspI', 2161), ('PSAV001.0321.00001.C001_02327', 'T2SS_gspJ', 2162), ('PSAV001.0321.00001.C001_02328', 'T2SS_gspK', 2163), ('PSAV001.0321.00001.C001_02329', 'T2SS_gspL', 2164), ('PSAV001.0321.00001.C001_02330', 'T2SS_gspM', 2165), ('PSAV001.0321.00001.C001_02332', 'T2SS_gspD', 2167)], [('PSAV001.0321.00001.C001_01018', 'T4P_pilD', 926)]
occ = 1
wholeness = 0.786
loci nb = 1
score = 7.560

mandatory genes:
	- T2SS_gspD: 1 (T2SS_gspD)
	- T2SS_gspE: 1 (T2SS_gspE)
	- T2SS_gspF: 1 (T2SS_gspF)
	- T2SS_gspG: 1 (T2SS_gspG)
	- T2SS_gspC: 0 ()
	- T2SS_gspO: 1 (T4P_pilD [PSAV001.0321.00001.C001_T4P_11, PSAV001.0321.00001.C001_T4P_12, PSAV001.0321.00001.C001_T4P_3, PSAV001.0321.00001.C001_T4P_5, PSAV001.0321.00001.C001_T4P_6, PSAV001.0321.00001.C001_T4P_7, PSAV001.0321.00001.C001_T4P_9])

accessory genes:
	- T2SS_gspM: 1 (T2SS_gspM)
	- T2SS_gspH: 1 (T2SS_gspH)
	- T2SS_gspI: 1 (T2SS_gspI)
	- T2SS_gspJ: 1 (T2SS_gspJ)
	- T2SS_gspK: 1 (T2SS_gspK)
	- T2SS_gspN: 0 ()
	- T2SS_gspL: 1 (T2SS_gspL)
	- Tad_tadD: 0 ()

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_T2SS_1
model = TFF-SF/T2SS
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_02322', 'T2SS_gspE', 2157), ('PSAV001.0321.00001.C001_02323', 'T2SS_gspF', 2158), ('PSAV001.0321.00001.C001_02324', 'T2SS_gspG', 2159), ('PSAV001.0321.00001.C001_02325', 'T2SS_gspH', 2160), ('PSAV001.0321.00001.C001_02326', 'T2SS_gspI', 2161), ('PSAV001.0321.00001.C001_02327', 'T2SS_gspJ', 2162), ('PSAV001.0321.00001.C001_02328', 'T2SS_gspK', 2163), ('PSAV001.0321.00001.C001_02329', 'T2SS_gspL', 2164), ('PSAV001.0321.00001.C001_02330', 'T2SS_gspM', 2165), ('PSAV001.0321.00001.C001_02332', 'T2SS_gspD', 2167)]
occ = 1
wholeness = 0.714
loci nb = 1
score = 7.000

mandatory genes:
	- T2SS_gspD: 1 (T2SS_gspD)
	- T2SS_gspE: 1 (T2SS_gspE)
	- T2SS_gspF: 1 (T2SS_gspF)
	- T2SS_gspG: 1 (T2SS_gspG)
	- T2SS_gspC: 0 ()
	- T2SS_gspO: 0 ()

accessory genes:
	- T2SS_gspM: 1 (T2SS_gspM)
	- T2SS_gspH: 1 (T2SS_gspH)
	- T2SS_gspI: 1 (T2SS_gspI)
	- T2SS_gspJ: 1 (T2SS_gspJ)
	- T2SS_gspK: 1 (T2SS_gspK)
	- T2SS_gspN: 0 ()
	- T2SS_gspL: 1 (T2SS_gspL)
	- Tad_tadD: 0 ()

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_Tad_14
model = TFF-SF/Tad
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_04742', 'Tad_tadE', 4431), ('PSAV001.0321.00001.C001_04743', 'Tad_tadV', 4432)], [('PSAV001.0321.00001.C001_04756', 'Tad_flp', 4445), ('PSAV001.0321.00001.C001_04757', 'Tad_rcpC', 4446), ('PSAV001.0321.00001.C001_04758', 'Tad_rcpA', 4447), ('PSAV001.0321.00001.C001_04759', 'Tad_tadZ', 4448), ('PSAV001.0321.00001.C001_04760', 'Tad_tadA', 4449), ('PSAV001.0321.00001.C001_04761', 'Tad_tadB', 4450), ('PSAV001.0321.00001.C001_04762', 'Tad_tadC', 4451), ('PSAV001.0321.00001.C001_04763', 'Tad_tadD', 4452)]
occ = 1
wholeness = 0.833
loci nb = 2
score = 8.500

mandatory genes:
	- Tad_rcpA: 1 (Tad_rcpA)
	- Tad_tadA: 1 (Tad_tadA)
	- Tad_tadB: 1 (Tad_tadB)
	- Tad_tadC: 1 (Tad_tadC)
	- Tad_tadV: 1 (Tad_tadV)
	- Tad_tadZ: 1 (Tad_tadZ)
	- Tad_flp: 1 (Tad_flp)

accessory genes:
	- Tad_tadE: 1 (Tad_tadE)
	- Tad_tadF: 0 ()
	- Tad_tadD: 1 (Tad_tadD)
	- Tad_rcpB: 0 ()
	- Tad_rcpC: 1 (Tad_rcpC)

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_Tad_13
model = TFF-SF/Tad
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_04756', 'Tad_flp', 4445), ('PSAV001.0321.00001.C001_04757', 'Tad_rcpC', 4446), ('PSAV001.0321.00001.C001_04758', 'Tad_rcpA', 4447), ('PSAV001.0321.00001.C001_04759', 'Tad_tadZ', 4448), ('PSAV001.0321.00001.C001_04760', 'Tad_tadA', 4449), ('PSAV001.0321.00001.C001_04761', 'Tad_tadB', 4450), ('PSAV001.0321.00001.C001_04762', 'Tad_tadC', 4451), ('PSAV001.0321.00001.C001_04763', 'Tad_tadD', 4452)]
occ = 1
wholeness = 0.667
loci nb = 1
score = 7.000

mandatory genes:
	- Tad_rcpA: 1 (Tad_rcpA)
	- Tad_tadA: 1 (Tad_tadA)
	- Tad_tadB: 1 (Tad_tadB)
	- Tad_tadC: 1 (Tad_tadC)
	- Tad_tadV: 0 ()
	- Tad_tadZ: 1 (Tad_tadZ)
	- Tad_flp: 1 (Tad_flp)

accessory genes:
	- Tad_tadE: 0 ()
	- Tad_tadF: 0 ()
	- Tad_tadD: 1 (Tad_tadD)
	- Tad_rcpB: 0 ()
	- Tad_rcpC: 1 (Tad_rcpC)

neutral genes:

============================================================
system id = PSAV001.0321.00001.C001_T4P_8
model = TFF-SF/T4P
replicon = PSAV001.0321.00001.C001
clusters = [('PSAV001.0321.00001.C001_05037', 'MSH_mshM', 4719), ('PSAV001.0321.00001.C001_05040', 'T4P_pilQ', 4722), ('PSAV001.0321.00001.C001_05041', 'T4P_pilP', 4723), ('PSAV001.0321.00001.C001_05042', 'T4P_pilO', 4724), ('PSAV001.0321.00001.C001_05043', 'T4P_pilN', 4725), ('PSAV001.0321.00001.C001_05044', 'T4P_pilM', 4726)], [('PSAV001.0321.00001.C001_04959', 'T4P_pilT', 4643)]
occ = 1
wholeness = 0.389
loci nb = 1
score = 5.200

mandatory genes:
	- T4P_pilE: 0 ()
	- T4P_pilB: 0 ()
	- T4P_pilC: 0 ()
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 0 ()

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 1 (MSH_mshM)

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T2SS_522
model = TFF-SF/T2SS
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00037', 'Tad_tadD', 7362), ('XAOR001.0321.00001.C001_00040', 'Tad_tadD', 7365)], [('XAOR001.0321.00001.C001_03012', 'T2SS_gspD', 9820), ('XAOR001.0321.00001.C001_03013', 'T2SS_gspN', 9821), ('XAOR001.0321.00001.C001_03014', 'T2SS_gspM', 9822), ('XAOR001.0321.00001.C001_03015', 'T2SS_gspL', 9823), ('XAOR001.0321.00001.C001_03016', 'T2SS_gspK', 9824), ('XAOR001.0321.00001.C001_03017', 'T2SS_gspJ', 9825), ('XAOR001.0321.00001.C001_03018', 'T2SS_gspI', 9826), ('XAOR001.0321.00001.C001_03019', 'T2SS_gspH', 9827), ('XAOR001.0321.00001.C001_03020', 'T2SS_gspG', 9828), ('XAOR001.0321.00001.C001_03021', 'T2SS_gspF', 9829), ('XAOR001.0321.00001.C001_03023', 'T2SS_gspE', 9831)], [('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)]
occ = 1
wholeness = 0.929
loci nb = 2
score = 8.560

mandatory genes:
	- T2SS_gspD: 1 (T2SS_gspD)
	- T2SS_gspE: 1 (T2SS_gspE)
	- T2SS_gspF: 1 (T2SS_gspF)
	- T2SS_gspG: 1 (T2SS_gspG)
	- T2SS_gspC: 0 ()
	- T2SS_gspO: 1 (T4P_pilD [XAOR001.0321.00001.C001_T4P_525, XAOR001.0321.00001.C001_T4P_526, XAOR001.0321.00001.C001_T4P_527, XAOR001.0321.00001.C001_T4P_529, XAOR001.0321.00001.C001_T4P_530, XAOR001.0321.00001.C001_T4P_531, XAOR001.0321.00001.C001_T4P_532, XAOR001.0321.00001.C001_T4P_533, XAOR001.0321.00001.C001_T4P_536, XAOR001.0321.00001.C001_T4P_537, XAOR001.0321.00001.C001_T4P_538, XAOR001.0321.00001.C001_T4P_540, XAOR001.0321.00001.C001_T4P_541, XAOR001.0321.00001.C001_T4P_542, XAOR001.0321.00001.C001_T4P_543])

accessory genes:
	- T2SS_gspM: 1 (T2SS_gspM)
	- T2SS_gspH: 1 (T2SS_gspH)
	- T2SS_gspI: 1 (T2SS_gspI)
	- T2SS_gspJ: 1 (T2SS_gspJ)
	- T2SS_gspK: 1 (T2SS_gspK)
	- T2SS_gspN: 1 (T2SS_gspN)
	- T2SS_gspL: 1 (T2SS_gspL)
	- Tad_tadD: 2 (Tad_tadD, Tad_tadD)

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T2SS_520
model = TFF-SF/T2SS
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00037', 'Tad_tadD', 7362), ('XAOR001.0321.00001.C001_00040', 'Tad_tadD', 7365)], [('XAOR001.0321.00001.C001_03012', 'T2SS_gspD', 9820), ('XAOR001.0321.00001.C001_03013', 'T2SS_gspN', 9821), ('XAOR001.0321.00001.C001_03014', 'T2SS_gspM', 9822), ('XAOR001.0321.00001.C001_03015', 'T2SS_gspL', 9823), ('XAOR001.0321.00001.C001_03016', 'T2SS_gspK', 9824), ('XAOR001.0321.00001.C001_03017', 'T2SS_gspJ', 9825), ('XAOR001.0321.00001.C001_03018', 'T2SS_gspI', 9826), ('XAOR001.0321.00001.C001_03019', 'T2SS_gspH', 9827), ('XAOR001.0321.00001.C001_03020', 'T2SS_gspG', 9828), ('XAOR001.0321.00001.C001_03021', 'T2SS_gspF', 9829), ('XAOR001.0321.00001.C001_03023', 'T2SS_gspE', 9831)]
occ = 1
wholeness = 0.857
loci nb = 2
score = 8.000

mandatory genes:
	- T2SS_gspD: 1 (T2SS_gspD)
	- T2SS_gspE: 1 (T2SS_gspE)
	- T2SS_gspF: 1 (T2SS_gspF)
	- T2SS_gspG: 1 (T2SS_gspG)
	- T2SS_gspC: 0 ()
	- T2SS_gspO: 0 ()

accessory genes:
	- T2SS_gspM: 1 (T2SS_gspM)
	- T2SS_gspH: 1 (T2SS_gspH)
	- T2SS_gspI: 1 (T2SS_gspI)
	- T2SS_gspJ: 1 (T2SS_gspJ)
	- T2SS_gspK: 1 (T2SS_gspK)
	- T2SS_gspN: 1 (T2SS_gspN)
	- T2SS_gspL: 1 (T2SS_gspL)
	- Tad_tadD: 2 (Tad_tadD, Tad_tadD)

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_543
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)], [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)], [('XAOR001.0321.00001.C001_03253', 'T4P_pilA', 10027)]
occ = 1
wholeness = 0.889
loci nb = 4
score = 11.350

mandatory genes:
	- T4P_pilE: 2 (T4P_pilE, T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_532
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)], [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)]
occ = 1
wholeness = 0.833
loci nb = 4
score = 11.000

mandatory genes:
	- T4P_pilE: 2 (T4P_pilE, T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_540
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)], [('XAOR001.0321.00001.C001_03253', 'T4P_pilA', 10027)]
occ = 1
wholeness = 0.667
loci nb = 3
score = 9.850

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_541
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)], [('XAOR001.0321.00001.C001_03253', 'T4P_pilA', 10027)]
occ = 1
wholeness = 0.778
loci nb = 3
score = 9.850

mandatory genes:
	- T4P_pilE: 2 (T4P_pilE, T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 0 ()
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_529
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)]
occ = 1
wholeness = 0.611
loci nb = 3
score = 9.500

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_530
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)]
occ = 1
wholeness = 0.722
loci nb = 3
score = 9.500

mandatory genes:
	- T4P_pilE: 2 (T4P_pilE, T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 0 ()
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_539
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)], [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)], [('XAOR001.0321.00001.C001_03253', 'T4P_pilA', 10027)]
occ = 1
wholeness = 0.722
loci nb = 3
score = 8.850

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 0 ()
	- T4P_pilC: 0 ()
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 0 ()

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_528
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)], [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)]
occ = 1
wholeness = 0.667
loci nb = 3
score = 8.500

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 0 ()
	- T4P_pilC: 0 ()
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 0 ()

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_536
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)], [('XAOR001.0321.00001.C001_03253', 'T4P_pilA', 10027)]
occ = 1
wholeness = 0.556
loci nb = 2
score = 8.350

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 0 ()
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_525
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)]
occ = 1
wholeness = 0.500
loci nb = 2
score = 8.000

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 0 ()
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_535
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)], [('XAOR001.0321.00001.C001_03253', 'T4P_pilA', 10027)]
occ = 1
wholeness = 0.611
loci nb = 2
score = 7.350

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 0 ()
	- T4P_pilC: 0 ()
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 0 ()
	- T4P_pilD: 0 ()

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_524
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)]
occ = 1
wholeness = 0.556
loci nb = 2
score = 7.000

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 0 ()
	- T4P_pilC: 0 ()
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 0 ()
	- T4P_pilD: 0 ()

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_534
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)], [('XAOR001.0321.00001.C001_03253', 'T4P_pilA', 10027)]
occ = 1
wholeness = 0.444
loci nb = 2
score = 5.850

mandatory genes:
	- T4P_pilE: 0 ()
	- T4P_pilB: 0 ()
	- T4P_pilC: 0 ()
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 0 ()

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_523
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00240', 'T4P_pilM', 7530), ('XAOR001.0321.00001.C001_00241', 'T4P_pilN', 7531), ('XAOR001.0321.00001.C001_00242', 'T4P_pilO', 7532), ('XAOR001.0321.00001.C001_00243', 'T4P_pilP', 7533), ('XAOR001.0321.00001.C001_00244', 'T4P_pilQ', 7534)], [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)]
occ = 1
wholeness = 0.389
loci nb = 2
score = 5.500

mandatory genes:
	- T4P_pilE: 0 ()
	- T4P_pilB: 0 ()
	- T4P_pilC: 0 ()
	- T4P_pilO: 1 (T4P_pilO)
	- T4P_pilQ: 1 (T4P_pilQ)
	- T4P_pilN: 1 (T4P_pilN)
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 0 ()

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 1 (T4P_pilM)
	- T4P_pilP: 1 (T4P_pilP)
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_542
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)], [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)], [('XAOR001.0321.00001.C001_03253', 'T4P_pilA', 10027)]
occ = 1
wholeness = 0.611
loci nb = 3
score = 7.350

mandatory genes:
	- T4P_pilE: 2 (T4P_pilE, T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 0 ()
	- T4P_pilQ: 0 ()
	- T4P_pilN: 0 ()
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 0 ()
	- T4P_pilP: 0 ()
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_531
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)], [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)]
occ = 1
wholeness = 0.556
loci nb = 3
score = 7.000

mandatory genes:
	- T4P_pilE: 2 (T4P_pilE, T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 0 ()
	- T4P_pilQ: 0 ()
	- T4P_pilN: 0 ()
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 0 ()
	- T4P_pilP: 0 ()
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_537
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)], [('XAOR001.0321.00001.C001_03253', 'T4P_pilA', 10027)]
occ = 1
wholeness = 0.389
loci nb = 2
score = 5.850

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 0 ()
	- T4P_pilQ: 0 ()
	- T4P_pilN: 0 ()
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 0 ()
	- T4P_pilP: 0 ()
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_526
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00601', 'T4P_pilU', 7819), ('XAOR001.0321.00001.C001_00602', 'T4P_pilT', 7820)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)]
occ = 1
wholeness = 0.333
loci nb = 2
score = 5.500

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 0 ()
	- T4P_pilQ: 0 ()
	- T4P_pilN: 0 ()
	- T4P_pilT: 1 (T4P_pilT)
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 0 ()
	- T4P_pilP: 0 ()
	- T4P_pilU: 1 (T4P_pilU)
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_538
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)], [('XAOR001.0321.00001.C001_03253', 'T4P_pilA', 10027)]
occ = 1
wholeness = 0.500
loci nb = 2
score = 5.850

mandatory genes:
	- T4P_pilE: 2 (T4P_pilE, T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 0 ()
	- T4P_pilQ: 0 ()
	- T4P_pilN: 0 ()
	- T4P_pilT: 0 ()
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 0 ()
	- T4P_pilP: 0 ()
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_527
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_00872', 'T4P_fimT', 8028), ('XAOR001.0321.00001.C001_00873', 'T4P_pilV', 8029), ('XAOR001.0321.00001.C001_00874', 'T4P_pilW', 8030), ('XAOR001.0321.00001.C001_00876', 'T4P_pilY', 8032), ('XAOR001.0321.00001.C001_00877', 'T4P_pilE', 8033), ('XAOR001.0321.00001.C001_00879', 'T4P_fimT', 8034)], [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)]
occ = 1
wholeness = 0.444
loci nb = 2
score = 5.500

mandatory genes:
	- T4P_pilE: 2 (T4P_pilE, T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 0 ()
	- T4P_pilQ: 0 ()
	- T4P_pilN: 0 ()
	- T4P_pilT: 0 ()
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 0 ()
	- T4P_pilV: 1 (T4P_pilV)
	- T4P_pilY: 1 (T4P_pilY)
	- T4P_pilW: 1 (T4P_pilW)
	- T4P_pilX: 0 ()
	- T4P_fimT: 2 (T4P_fimT, T4P_fimT)
	- T4P_pilM: 0 ()
	- T4P_pilP: 0 ()
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T4P_533
model = TFF-SF/T4P
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_02929', 'T4P_pilB', 9754), ('XAOR001.0321.00001.C001_02933', 'T4P_pilE', 9758), ('XAOR001.0321.00001.C001_02934', 'T4P_pilC', 9759), ('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)], [('XAOR001.0321.00001.C001_03253', 'T4P_pilA', 10027)]
occ = 1
wholeness = 0.278
loci nb = 1
score = 4.350

mandatory genes:
	- T4P_pilE: 1 (T4P_pilE)
	- T4P_pilB: 1 (T4P_pilB)
	- T4P_pilC: 1 (T4P_pilC)
	- T4P_pilO: 0 ()
	- T4P_pilQ: 0 ()
	- T4P_pilN: 0 ()
	- T4P_pilT: 0 ()
	- T4P_pilD: 1 (T4P_pilD [XAOR001.0321.00001.C001_T2SS_521, XAOR001.0321.00001.C001_T2SS_522])

accessory genes:
	- T4P_pilA: 1 (T4P_pilA)
	- T4P_pilV: 0 ()
	- T4P_pilY: 0 ()
	- T4P_pilW: 0 ()
	- T4P_pilX: 0 ()
	- T4P_fimT: 0 ()
	- T4P_pilM: 0 ()
	- T4P_pilP: 0 ()
	- T4P_pilU: 0 ()
	- MSH_mshM: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T2SS_521
model = TFF-SF/T2SS
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_03012', 'T2SS_gspD', 9820), ('XAOR001.0321.00001.C001_03013', 'T2SS_gspN', 9821), ('XAOR001.0321.00001.C001_03014', 'T2SS_gspM', 9822), ('XAOR001.0321.00001.C001_03015', 'T2SS_gspL', 9823), ('XAOR001.0321.00001.C001_03016', 'T2SS_gspK', 9824), ('XAOR001.0321.00001.C001_03017', 'T2SS_gspJ', 9825), ('XAOR001.0321.00001.C001_03018', 'T2SS_gspI', 9826), ('XAOR001.0321.00001.C001_03019', 'T2SS_gspH', 9827), ('XAOR001.0321.00001.C001_03020', 'T2SS_gspG', 9828), ('XAOR001.0321.00001.C001_03021', 'T2SS_gspF', 9829), ('XAOR001.0321.00001.C001_03023', 'T2SS_gspE', 9831)], [('XAOR001.0321.00001.C001_02935', 'T4P_pilD', 9760)]
occ = 1
wholeness = 0.857
loci nb = 1
score = 8.060

mandatory genes:
	- T2SS_gspD: 1 (T2SS_gspD)
	- T2SS_gspE: 1 (T2SS_gspE)
	- T2SS_gspF: 1 (T2SS_gspF)
	- T2SS_gspG: 1 (T2SS_gspG)
	- T2SS_gspC: 0 ()
	- T2SS_gspO: 1 (T4P_pilD [XAOR001.0321.00001.C001_T4P_525, XAOR001.0321.00001.C001_T4P_526, XAOR001.0321.00001.C001_T4P_527, XAOR001.0321.00001.C001_T4P_529, XAOR001.0321.00001.C001_T4P_530, XAOR001.0321.00001.C001_T4P_531, XAOR001.0321.00001.C001_T4P_532, XAOR001.0321.00001.C001_T4P_533, XAOR001.0321.00001.C001_T4P_536, XAOR001.0321.00001.C001_T4P_537, XAOR001.0321.00001.C001_T4P_538, XAOR001.0321.00001.C001_T4P_540, XAOR001.0321.00001.C001_T4P_541, XAOR001.0321.00001.C001_T4P_542, XAOR001.0321.00001.C001_T4P_543])

accessory genes:
	- T2SS_gspM: 1 (T2SS_gspM)
	- T2SS_gspH: 1 (T2SS_gspH)
	- T2SS_gspI: 1 (T2SS_gspI)
	- T2SS_gspJ: 1 (T2SS_gspJ)
	- T2SS_gspK: 1 (T2SS_gspK)
	- T2SS_gspN: 1 (T2SS_gspN)
	- T2SS_gspL: 1 (T2SS_gspL)
	- Tad_tadD: 0 ()

neutral genes:

============================================================
system id = XAOR001.0321.00001.C001_T2SS_519
model = TFF-SF/T2SS
replicon = XAOR001.0321.00001.C001
clusters = [('XAOR001.0321.00001.C001_03012', 'T2SS_gspD', 9820), ('XAOR001.0321.00001.C001_03013', 'T2SS_gspN', 9821), ('XAOR001.0321.00001.C001_03014', 'T2SS_gspM', 9822), ('XAOR001.0321.00001.C001_03015', 'T2SS_gspL', 9823), ('XAOR001.0321.00001.C001_03016', 'T2SS_gspK', 9824), ('XAOR001.0321.00001.C001_03017', 'T2SS_gspJ', 9825), ('XAOR001.0321.00001.C001_03018', 'T2SS_gspI', 9826), ('XAOR001.0321.00001.C001_03019', 'T2SS_gspH', 9827), ('XAOR001.0321.00001.C001_03020', 'T2SS_gspG', 9828), ('XAOR001.0321.00001.C001_03021', 'T2SS_gspF', 9829), ('XAOR001.0321.00001.C001_03023', 'T2SS_gspE', 9831)]
occ = 1
wholeness = 0.786
loci nb = 1
score = 7.500

mandatory genes:
	- T2SS_gspD: 1 (T2SS_gspD)
	- T2SS_gspE: 1 (T2SS_gspE)
	- T2SS_gspF: 1 (T2SS_gspF)
	- T2SS_gspG: 1 (T2SS_gspG)
	- T2SS_gspC: 0 ()
	- T2SS_gspO: 0 ()

accessory genes:
	- T2SS_gspM: 1 (T2SS_gspM)
	- T2SS_gspH: 1 (T2SS_gspH)
	- T2SS_gspI: 1 (T2SS_gspI)
	- T2SS_gspJ: 1 (T2SS_gspJ)
	- T2SS_gspK: 1 (T2SS_gspK)
	- T2SS_gspN: 1 (T2SS_gspN)
	- T2SS_gspL: 1 (T2SS_gspL)
	- Tad_tadD: 0 ()

neutral genes:

============================================================
# WARNING Loner: there is only 1 occurrence(s) of loner 'T4P_pilT' and 6 potential systems [PSAV001.0321.00001.C001_T4P_12, PSAV001.0321.00001.C001_T4P_10, PSAV001.0321.00001.C001_T4P_9, PSAV001.0321.00001.C001_T4P_11, PSAV001.0321.00001.C001_T4P_7, PSAV001.0321.00001.C001_T4P_8]
# WARNING Loner: there is only 1 occurrence(s) of loner 'T4P_pilD' and 2 potential systems [XAOR001.0321.00001.C001_T2SS_522, XAOR001.0321.00001.C001_T2SS_521]
# WARNING Loner: there is only 1 occurrence(s) of loner 'T4P_pilA' and 11 potential systems [XAOR001.0321.00001.C001_T4P_543, XAOR001.0321.00001.C001_T4P_540, XAOR001.0321.00001.C001_T4P_541, XAOR001.0321.00001.C001_T4P_539, XAOR001.0321.00001.C001_T4P_536, XAOR001.0321.00001.C001_T4P_535, XAOR001.0321.00001.C001_T4P_534, XAOR001.0321.00001.C001_T4P_542, XAOR001.0321.00001.C001_T4P_537, XAOR001.0321.00001.C001_T4P_538, XAOR001.0321.00001.C001_T4P_533]
