AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID034_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391177
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	fliF	214	flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein
#1	atpD	26	membrane-bound ATP synthase, F1 sector, beta-subunit
#2	atpG	50	membrane-bound ATP synthase, F1 sector, gamma-subunit
#3	atpF	61	membrane-bound ATP synthase, F0 sector, subunit b
#4	atpE	46	membrane-bound ATP synthase, F0 sector, subunit c
#5	atpI	300	membrane-bound ATP synthase, dispensable protein, affects expression of atpB

Motif 1
 TCTCGTCTCCCGGATAATTTCTGGTAGCAA	0	9	1
CCGCCAATAAACCCGTTTTTTTGTTGCTATT	0	74	0
AAATTGACGCTCCCATTATTTGTGCTTTCGT	0	115	0
TGATTATGGACGGCGTTATTGGCAAAGTGGA	0	178	0
          ACAGGTTATTTCGTAGAGGAT	1	0	1
         AAGGCATCATTTGCCAAGTAAA	5	1	1
ACCAGTGTTTACGCGTTATTTACAGTTTTTC	5	85	1
TACGGTGCGCCCCCGTGATTTCAAACAATAA	5	196	0
CGGGGGCGCACCGTATAATTTGACCGCTTTT	5	212	1
          ****** ****
MAP Score: 6.10375

Motif 2
GATAATTTCTGGTAGCAAAGCCTACCAGTA	0	22	1
GGCGCTAAATAGCAACAAAAAAACGGGTTT	0	67	1
GTCCATAATCAGCCACGAGGTGCGCG    	0	198	1
CCCTAAGGCAAGCCGCCAGACG        	2	2	0
CCTTAGGGCAGGCCGCAAGGCATTGAGGAG	2	24	1
GAACAGGGTTAGCAGAAAAGTCGCAATTGT	5	122	1
AACAATAAGTAGCCAAAAGGTGAATAAATG	5	174	0
CTTAGAGTCAAGCATCAAAAAGCGGTCAAA	5	230	0
CTTGACTCTAAGCCTTAAAGAAAGTTTTAT	5	248	1
          **********
MAP Score: 5.11092

Motif 3
CGGATAATTTCTGGTAGCAAAGCCTACCAGTAA	0	20	1
GTAGCAAAGCCTACCAGTAAGTCAATAAGACAA	0	33	1
TTTTTTCTATCCGCCAATAAACCCGTTTTTTTG	0	82	0
GTTTGCTGACCCGGGAGTGAGTCTTGTTCCACT	0	151	1
TTGTTCCACTTTGCCAATAACGCCGTCCATAAT	0	174	1
TGCCTTAGGGCAGGCCGCAAGGCATTGAGGAGA	2	22	1
TTTATTTACTTGGCAAATGATGCCTT       	5	3	0
CGCGTAAACACTGGTGATAAAGCGTGCTTCAGA	5	67	0
TCATGAAAAACTGTAAATAACGCGTAAACACTG	5	87	0
          * ** ***** **
MAP Score: 4.07604