#Annotation File Formatting for ClustAGE:
#
#Annotation files produced by newer versions of Spine (v0.2 or above) or AGEnt (v0.2 or above) will already be in the proper format. These file names will end with "accessory_loci.txt".
#
#Annotation files must have the following format to be used by ClustAGE:
#- Columns must be separated by single tabs (NOT any other whitespace)
#- Column 1:locusID of gene
#- Column 2:Source contig ID (from which accessory sequence was identified)
#- Column 3:Source start coordinate (1-based)
#- Column 4:Source stop coordinate (1-based)
#- Column 5:Strand on which the gene is encoded
#- Column 6:Accessory sequence ID (shoud match sequence IDs in accessory sequence file provided to ClustAGE)
#- Column 7:Accessory start coordinate (1-based)
#- Column 8:Accessory stop coordinate (1-based)
#- Column 9:% of gene represented in the accessory sequence
#- Column 10:Number of bases of the gene missing from the end(s) of an accessory segment. Values are separated by a comma. First value is the number of bases missing from the 5' end of the accessory segement, second value is the number of bases missing from the 3' end of the accessory segment.
#- Column 11:Gene product name
#
#
#Example:
#
locus_id	gen_contig_id	gen_contig_start	gen_contig_stop	strand	out_seq_id	out_seq_start	out_seq_stop	pct_locus	overhangs	product
PA0041	AE004091	51722	53521	+	PAO1_accessory_0001_length_2118	1	1800	16.97	8808,0	probable hemagglutinin
PA0053	AE004091	69272	69526	+	PAO1_accessory_0004_length_825	561	815	100.00	0,0	hypothetical protein
PA0092	AE004091	113288	113306	-	PAO1_accessory_0005_length_559	1	19	6.67	266,0	hypothetical protein
PA0093	AE004091	113303	113846	-	PAO1_accessory_0005_length_559	16	559	42.07	0,749	hypothetical protein
PA0098	AE004091	119268	120164	+	PAO1_accessory_0006_length_3307	1	897	86.42	141,0	hypothetical protein
PA0099	AE004091	120164	121324	+	PAO1_accessory_0006_length_3307	897	2057	100.00	0,0	hypothetical protein
PA0100	AE004091	121346	122266	+	PAO1_accessory_0006_length_3307	2079	2999	100.00	0,0	hypothetical protein
PA0101	AE004091	122248	122574	+	PAO1_accessory_0006_length_3307	2981	3307	26.20	0,921	hypothetical protein
PA0144	AE004091	164443	164460	-	PAO1_accessory_0007_length_44	27	44	2.87	0,609	hypothetical protein
PA0187	AE004091	213819	214634	+	PAO1_accessory_0008_length_2125	408	1223	100.00	0,0	hypothetical protein
PA0188	AE004091	214631	215512	+	PAO1_accessory_0008_length_2125	1220	2101	100.00	0,0	hypothetical protein
PA0202	AE004091	230543	232000	-	PAO1_accessory_0009_length_6627	8	1465	100.00	0,0	probable amidase
PA0203	AE004091	232066	233100	-	PAO1_accessory_0009_length_6627	1531	2565	100.00	0,0	probable binding protein component of ABC transporter
PA0204	AE004091	233123	233932	-	PAO1_accessory_0009_length_6627	2588	3397	100.00	0,0	probable permease of ABC transporter
PA0205	AE004091	233929	234849	-	PAO1_accessory_0009_length_6627	3394	4314	100.00	0,0	probable permease of ABC transporter
PA0206	AE004091	234875	235987	-	PAO1_accessory_0009_length_6627	4340	5452	100.00	0,0	probable ATP-binding component of ABC transporter
PA0207	AE004091	236218	237111	+	PAO1_accessory_0009_length_6627	5683	6576	100.00	0,0	probable transcriptional regulator
PA0257	AE004091	288384	289175	-	PAO1_accessory_0012_length_1170	50	841	100.00	0,0	hypothetical protein
PA0258	AE004091	289205	289390	-	PAO1_accessory_0012_length_1170	871	1056	100.00	0,0	hypothetical protein
PA0260	AE004091	291174	291397	-	PAO1_accessory_0013_length_224	1	224	10.41	20,1907	hypothetical protein
PA0445	AE004091	500104	501120	-	PAO1_accessory_0016_length_1391	276	1292	100.00	0,0	probable transposase