AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions024_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246917
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hypothetical	277	hypothetical protein
#1	hypothetical	94	hypothetical protein
#2	rfbU	21	mannosyltransferase B
#3	mtfB	48	Mannosyltransferase B
#4	regulatory	107	regulatory components of sensory transduction system
#5	lpxA	26	acyl-[acyl-carrier-protein]-UDP-N-acetylglucosam ine o-acyltransferase

Motif 1
          CAATTAATTTTGCTCACTGTTGATCA	3	32	0
TTCAGTTCAACTTCTACTTTTACTCAACTTTTCTTC	4	51	1
TAAAATGAATTCACTAGATTTGCTAAAATTCT    	1	72	1
        AATTTTGACATTTGCTAAGTATTGATCA	3	2	1
CAATTAATTGCTCCCAACTGTACTAACAGGTGTTGA	4	12	1
TGCCATTCATCAATCAATGTTGCTGAATGATCTGAT	0	230	0
GAAAAATCAGCATGTACGTGTAGTCATTATGCTAGA	0	161	1
AAGTATTCAGCATAAACTGTTGATCACCGTTGCCAC	1	25	1
TCATTTTATGCGCCCATCGGTGGCAACGGTGATCAA	1	44	0
CAGTTTATGCTGAATACTTTTGCCAATCTTAAAT  	1	8	0
      TTCTTGTTTAAAGGTAGTCACTTTACCTAG	0	4	1
GCTGATTTTTCAGAGATTTGTAATGATCTGGAATTG	0	136	0
          *    *  ********
MAP Score: 8.53324

Motif 2
CTTGTTTAAAGGTAGTCACTTTACCTAGATTA	0	12	1
TAATGAACGATGTACGCAATAGAGTTTGAAGC	0	81	1
TTCAGAGATTTGTAATGATCTGGAATTGTAAG	0	132	0
AGCATGTACGTGTAGTCATTATGCTAGATGGC	0	169	1
AGATGGCCATGGTAATGAATTGGAACTACGGG	0	194	1
GATTGGCAAAAGTATTCAGCATAAACTGTTGA	1	16	1
CGGTGGCAACGGTGATCAACAGTTTATGCTGA	1	31	0
GCAAATCTAGTGAATTCATTTTATGCGCCCAT	1	63	0
ACATTTGCTAAGTATTGATCAACAGTGAGCAA	3	17	1
AAGTAGAAGTTGAACTGAATTTTCAACACCTG	4	38	0
AACTTCTACTTTTACTCAACTTTTCTTCCCCC	4	59	1
          **** *** ***
MAP Score: 4.13673

Motif 3
ATCAACAGTTTATGCTGAATACTTTTGCCAATC	1	16	0
  CAATTAATTTTGCTCACTGTTGATCAATACT	3	27	0
ATCAATCAATGTTGCTGAATGATCTGATAAGGC	0	225	0
GTGTAGTCATTATGCTAGATGGCCATGGTAATG	0	178	1
AATTTTGACATTTGCTAAGTATTGATCAACAGT	3	10	1
TGCTCCCAACTGTACTAACAGGTGTTGAAAATT	4	20	1
ATCTTGTAGATCTGCTTCAAACTCTATTGCGTA	0	93	0
ATTCACTAGATTTGCTAAAATTCT         	1	80	1
GACATTTCTTTATACATAATAATCTAGATAATC	0	39	0
TTGAAGCAGATCTACAAGATGGTGTTCTTACAA	0	106	1
AACTTCTACTTTTACTCAACTTTTCTTCCCCCT	4	59	1
AAGTAGAAGTTGAACTGAATTTTCAACACCTGT	4	37	0
          * **** **** *
MAP Score: 1.32128

Motif 4
GAGATTTGTAATGATCTGGAATTGTAAGAACACCAT	0	124	0
TAGCATAATGACTACACGTACATGCTGATTTTTCAG	0	159	0
TAGTCATTATGCTAGATGGCCATGGTAATGAATTGG	0	181	1
GGCAACGGTGATCAACAGTTTATGCTGAATACTTTT	1	23	0
CATAAAATGAATTCACTAGATTTGCTAAAATTCT  	1	70	1
TCCCAACTGTACTAACAGGTGTTGAAAATTCAGTTC	4	23	1
   GGCGATCGCCTGCGGGAATTGGTGGAGGGGGAA	4	84	0
        AGATTAGCAGGCATTGTACCCCTGGA  	5	8	0
          ** * * **  *** *
MAP Score: 0.0351004