AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions024_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246926
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hypothetical	300	hypothetical protein
#1	rfbE	56	perosamine synthetase
#2	hypothetical	28	hypothetical protein
#3	hypothetical	277	hypothetical protein
#4	hypothetical	94	hypothetical protein
#5	rfbU	21	mannosyltransferase B
#6	mtfB	48	Mannosyltransferase B
#7	regulatory	107	regulatory components of sensory transduction system
#8	sensory	232	sensory transduction histidine kinase
#9	lpxA	26	acyl-[acyl-carrier-protein]-UDP-N-acetylglucosam ine o-acyltransferase

Motif 1
CTACACCAAGCCGTTGATCGCCATACAATGCC	0	21	1
TGTACTAGAATGATCGTTCGCCTCCCCACTAC	0	88	1
GTGTAGTGAATGGGTCATTTCCAAAACGAGCA	0	166	1
ATTGCGTACATCGTTCATTACCTAAAATCGAC	3	69	0
CCCGTAGTTCCAATTCATTACCATGGCCATCT	3	194	0
TCAGCATAAACTGTTGATCACCGTTGCCACCG	4	31	1
TTTTACTCAACTTTTCTTCCCCCTCCACCAAT	7	68	1
CCAATTCCCGCAGGCGATCGCC          	7	95	1
CCTAGGAGGATAGGCGATCGCCGGGGGGAGGT	8	131	1
CGCTGTGGCCCAGTCCTTTTCCAGCAAAGTTC	8	210	0
          * ******* **
MAP Score: 10.09

Motif 2
TGTTGGCGACAAAGTTGCCAATTGGCTATTA	0	241	0
TTCATCAATCAATGTTGCTGAATGATCTGAT	3	230	0
TATGCTGAATACTTTTGCCAATCTTAAAT  	4	8	0
TTCAGCATAAACTGTTGATCACCGTTGCCAC	4	30	1
TGAATTCACTAGATTTGCTAAAATTCT    	4	77	1
   AATTTTGACATTTGCTAAGTATTGATCA	6	7	1
     CAATTAATTTTGCTCACTGTTGATCA	6	32	0
TTCAACTTCTACTTTTACTCAACTTTTCTTC	7	56	1
TAAAGATGGCAAATTTGACCAAAACTCAACA	8	54	0
TCCCGTTCCAACTTTTGCTCCAAAACCTCCC	8	156	0
          * *********
MAP Score: 8.69834

Motif 3
     ACATCATCCTCGGAGGGATCATGCCAT	3	260	0
GCCTGCGGGAATTGGTGGAGGGGGAAGAAAAG	7	78	0
      GGCGATCGCCTGCGGGAATTGGTGGA	7	91	0
GATGGGTCAAATCCTAGGAGGATAGGCGATCG	8	119	1
AGGATAGGCGATCGCCGGGGGGAGGTTTTGGA	8	137	1
GAACGGGAAGATTGTCTGCGGGCAATTGCGAG	8	179	1
          **** *** ***
MAP Score: 7.77732

Motif 4
ATGGTAGTGGGGAGGCGAACGATCATTCTAGTA	0	90	0
GTCATGTTTTAGAATGGCATGATTTACATCAAC	0	202	1
GTCGATTTTAGGTAATGAACGATGTACGCAATA	3	69	1
GTAATGATCTGGAATTGTAAGAACACCATCTTG	3	120	0
ATCAATCAATGTTGCTGAATGATCTGATAAGGC	3	225	0
CATTGATTGATGAATGGCATGATCCCTCCGAGG	3	247	1
GGGAATTGGTGGAGGGGGAAGAAAAGTTGAGTA	7	71	0
AGCAAAAGTTGGAACGGGAAGATTGTCTGCGGG	8	168	1
          **** ** * ***
MAP Score: 5.80775

Motif 5
TTGGCGACAAAGTTGCCAATTGGCTATTAACT	0	238	0
TTGGCAACTTTGTCGCCAACAAGAAGATCTAA	0	251	1
TAATGAACGATGTACGCAATAGAGTTTGAAGC	3	81	1
ATTCATTTTATGCGCCCATCGGTGGCAACGGT	4	50	0
CCCAATTAATTGCTCCCAACTGTACTAACAGG	7	10	1
CACCAATTCCCGCAGGCGATCGCC        	7	93	1
ACTTTGGGGCTGTCCCCAACTGGTGAGATGGG	8	93	1
GAAGATTGTCTGCGGGCAATTGCGAGAACTTT	8	185	1
          *** ****** *
MAP Score: 4.26673

Motif 6
TGTACTAACAGGTGTTGAAAATTCAGTTCAAC	7	30	1
TCAACGGCTTGGTGTAGTAAATGCGGGA    	0	6	0
TATGCTGAATACTTTTGCCAATCTTAAAT   	4	7	0
AATCGAAACAGGTGTAGTGAATGGGTCATTTC	0	155	1
CACCTGTTTCGATTTCGACAATGATTTCATAT	0	137	0
GGTAATGAACGATGTACGCAATAGAGTTTGAA	3	79	1
       AGAATTTTAGCAAATCTAGTGAATT	4	79	0
ACGTAATGCTCGTTTTGGAAATGACCCATTCA	0	172	0
TCAGCATGTACGTGTAGTCATTATGCTAGATG	3	167	1
ATTAACTCGGGTTGATGTAAATCATGCCATTC	0	213	0
TGTTGGCGACAAAGTTGCCAATTGGCTATTAA	0	240	0
          AATTTTGACATTTGCTAAGTAT	6	0	1
AGAAATGTCGATTTTAGGTAATGAACGATGTA	3	63	1
          * ***** ****
MAP Score: 3.20404

Motif 7
ACGGTGAATATGAAATCATTGTCGAAATCG	0	130	1
TCTTACAATTCCAGATCATTACAAATCTCT	3	131	1
GCCCGTAGTTCCAATTCATTACCATGGCCA	3	197	0
ACGGGCCTTATCAGATCATTCAGCAACATT	3	221	1
GCAAATCTAGTGAATTCATTTTATGCGCCC	4	65	0
         CCCAATTAATTGCTCCCAACT	7	1	1
          **********
MAP Score: 2.94007

Motif 8
AACGACTAATAATGGGCATTGTATGGCGATCAACGGCTTGGTG	0	24	0
ACTTTACCTAGATTATCTAGATTATTATGTATAAAGAAATGTC	3	29	1
CATTATGCTAGATGGCCATGGTAATGAATTGGAACTACGGGCC	3	185	1
    ATTTAAGATTGGCAAAAGTATTCAGCATAAACTGTTGAT	4	6	1
CGTTGCCACCGATGGGCGCATAAAATGAATTCACTAGATTTGC	4	52	1
       GGCGATCGCCTGCGGGAATTGGTGGAGGGGGAAGAA	7	81	0
       GCTGATTGTCTAGGAATTTGTTTATAGTTAGACTAC	8	3	1
GAGGATAGGCGATCGCCGGGGGGAGGTTTTGGAGCAAAAGTTG	8	136	1
          *** * *   *  * *   *  *
MAP Score: 2.4701

Motif 9
AACGACTAATAATGGGCATTGTATGGCGATCAACGGCTTGG	0	26	0
GGAATCACAATCTGCATGTACTAGAATGATCGTTCGCCTCC	0	72	1
ATACGGTGAATATGAAATCATTGTCGAAATCGAAACAGGTG	0	128	1
CATGTTTTAGAATGGCATGATTTACATCAACCCGAGTTAAT	0	204	1
TTAATAGCCAATTGGCAACTTTGTCGCCAACAAGAAGATCT	0	240	1
TTCAAACTCTATTGCGTACATCGTTCATTACCTAAAATCGA	3	70	0
ATGGTAATGAATTGGAACTACGGGCCTTATCAGATCATTCA	3	202	1
GAATTCATTTTATGCGCCCATCGGTGGCAACGGTGATCAAC	4	43	0
  CCCAATTAATTGCTCCCAACTGTACTAACAGGTGTTGAA	7	8	1
TTTGGTCAAATTTGCCATCTTTAAGGGTATCACTTTGGGGC	8	62	1
GCTGTCCCCAACTGGTGAGATGGGTCAAATCCTAGGAGGAT	8	101	1
CGGGGGGAGGTTTTGGAGCAAAAGTTGGAACGGGAAGATTG	8	152	1
GGGAAGATTGTCTGCGGGCAATTGCGAGAACTTTGCTGGAA	8	183	1
          * ***   **   *    ***
MAP Score: 1.45391

Motif 10
ACTACACCAAGCCGTTGATCGCCATACAATGCC	0	20	1
ATATGAAATCATTGTCGAAATCGAAACAGGTGT	0	137	1
GGTGTAGTGAATGGGTCATTTCCAAAACGAGCA	0	165	1
ACCAATTCCCGCAGGCGATCGCC          	7	94	1
CATCTCACCAGTTGGGGACAGCCCCAAAGTGAT	8	90	0
AACTGGTGAGATGGGTCAAATCCTAGGAGGATA	8	110	1
TCCTAGGAGGATAGGCGATCGCCGGGGGGAGGT	8	130	1
AAGATTGTCTGCGGGCAATTGCGAGAACTTTGC	8	186	1
CGAGAACTTTGCTGGAAAAGGACTGGGCCACAG	8	207	1
      TCCAGGGGTACAATGCCTGCTAATCT 	9	4	1
          ** ** *** ***
MAP Score: 1.19949