AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile008_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243584
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CT386	280	predicted metal dependent hydrolase
#1	CT460	300	SWIB (YM74) complex protein
#2	CT472	300	hypothetical protein
#3	fliI	73	Flagellum-specific ATP Synthase
#4	fliF	272	Flagellar M-Ring Protein
#5	ftsK	300	Cell Division Protein FtsK

Motif 1
AATGTGATGTAGGTAAAGAAGATCTAGGGCTT	0	118	1
TCTAGGGCTTCGAACAGGAAAATACCTTCAGC	0	140	1
AATAGCTCTTTGAAAAAGAAGAGTTTAAAGTT	1	19	0
TGGAAATAACTGGCAAGGAAAATAGCTCTTTG	1	39	0
GAAATTGATCCCTAAGAGAAGATCATGTTACC	1	107	0
AGCCAAGTCTTCAGCAAGAAGAGAGGTAAAAG	1	178	0
ATAAAAGAGTTGCGAAGGAAGAGCCCTAAACT	1	245	1
GATGACTCCTAGTTAAAGAAGATGATAAGAAA	1	277	0
GCCACTTCCGCAAAAAAGAAGACATGAAGAAT	2	48	1
TTCCTATCTATTTTAAAGAAAAAATTGGAGGA	2	135	1
ATCTATATCGTTGAAAGGAAGAGTGTCTCATA	2	266	0
AGCCTCTTTTTGTTACAGAAGACAAAAGGGCT	4	72	1
CTTCTTCTTGTGAACAAGAAGAAAATTAGCAT	4	146	0
AAGAAAAGGATGAAAAAGAAGGCTTCTTCTTG	4	168	0
GCTAAGTATCCTACAAAGAAAAGGATGAAAAA	4	183	0
TTTTAGGAAACTATAAAGAAGGGCGAACGACG	5	120	0
GTAGCTTGTTATAACAGGAAAAATAAAAGAAT	5	163	0
          **  ********
MAP Score: 18.6226

Motif 2
AAATTTTTAAAAAGAGAGTTTAAAGAACGCT	0	46	1
CTCTTTGAAAAAGAAGAGTTTAAAGTTGGAT	1	15	0
AGAGTTGCGAAGGAAGAGCCCTAAACTTTTC	1	250	1
TTTACTTGTAGTAAAGAGTCCAATCAGAGTA	2	85	0
GAATTTGTAAGCTGAGAGGTTTTTTACTTGT	2	107	0
AGATAGAGAGGATAAGAGTTTTCTCTGATAA	2	168	0
TATCGTTGAAAGGAAGAGTGTCTCATATTCA	2	262	0
CTTCTGTAACAAAAAGAGGCTATTAAAAACA	4	62	0
GGCTCTTTTAATTGAGAGTCCCTTTTGAGCT	4	100	1
AATAGAGCAAGGGTAGAGCCCGCTAAGTATC	4	205	0
CTCAACCTATACGTAGAGCTTTTGTAAGAAC	4	237	1
        CAACGTAGAGCGCCTGCACGCTC	5	2	1
TAGCTCAGTTGGTTAGAGCGTCGGATTGTGG	5	64	1
TGCTAGGATCATTGAGAGCTTCCGCAATGAT	5	210	1
CGCTATTTCTGTTAAGAGTCCCTATCAGTTA	5	262	1
          * *********
MAP Score: 8.91938

Motif 3
CCTCGTGTGTGAAGAACCAGCTTATAGGAAAAAT	0	16	1
TATTACAGTGGCGGTGACAGCTAAAACACGCTCA	1	72	1
AGCAAGAAGAGAGGTAAAAGCGAATTAGAAAACG	1	164	0
AAAGAGTTGCGAAGGAAGAGCCCTAAACTTTTCT	1	248	1
GCGCTATCTTGAGGTGGTAGTGGAG         	2	1	0
CTTCTTTTTTGCGGAAGTGGCGGAATTGGTATAC	2	35	0
AAGAAGACATGAAGAATCAGCTTACTCTGATTGG	2	63	1
         AGCGGCATCAGCTACAAACATTACG	3	1	1
CGCTTATATGGAGGTGTTAGCCTATCATTGCGGA	5	230	0
          **** *  **** *
MAP Score: 5.44922

Motif 4
TCGTGTGTGAAGAACCAGCTTATAGGAAAAATTTTT	0	18	1
GGTGACAGCTAAAACACGCTCATGGTAACATGATCT	1	84	1
GAAGACATGAAGAATCAGCTTACTCTGATTGGACTC	2	65	1
CTTGTAGTAAAGAGTCCAATCAGAGTAAGCTGATTC	2	76	0
ACTACAAGTAAAAAACCTCTCAGCTTACAAATTCCT	2	104	1
GATTTATCAGAGAAAACTCTTATCCTCTCTATCTCA	2	165	1
CCTTATTGTAAGAAACCACTGAATATGAGACACTCT	2	243	1
GAGCAAGGGTAGAGCCCGCTAAGTATCCTACAAAGA	4	196	0
          **** ** ** *   *
MAP Score: 4.23862

Motif 5
GTCGAGGGGATCACGGAGGATA        	0	268	1
AAATAGCTCTTTGAAAAAGAAGAGTTTAAA	1	22	0
ATTTCCACTATTACAGTGGCGGTGACAGCT	1	64	1
CCTCGGACTATTACGCAAGAAATTGATCCC	1	127	0
ACCTCTCTTCTTGCTGAAGACTTGGCTATG	1	183	1
CATAAAAGAGTTGCGAAGGAAGAGCCCTAA	1	244	1
TGACTCCTAGTTAAAGAAGATGATAAGAAA	1	277	0
GTCTTCTTTTTTGCGGAAGTGGCGGAATTG	2	41	0
GGATAGGCTTTTGCAGAGACTTTGTTTGAG	2	213	0
CCTCTTTTTGTTACAGAAGACAAAAGGGCT	4	74	1
AAAGAAAAGGATGAAAAAGAAGGCTTCTTC	4	171	0
AAGTAAGTTCTTACAAAAGCTCTACGTATA	4	244	0
TAGCCTATCATTGCGGAAGCTCTCAATGAT	5	217	0
          **********
MAP Score: 1.97434