AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons023_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238236
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	guaB	300	Inosine 5'-monophosphase dehydrogenase
#1	ubiA	300	Benzoate Octaphenyltransferase
#2	yscU	300	Yop Translocation Protein U
#3	lcrE	28	Low Calcium Response E
#4	rl28	216	L28 Ribosomal Protein
#5	CPn0328	26	CT085 hypothetical protein
#6	CPn0329	92	Phopholipase D  Superfamily

Motif 1
TTGGGAATCTTACATAAAAATATGAGCGAAGTAGA	0	172	1
AAGCTCATCTGTGAGAAAAATTAAAGAAGCCTATC	0	210	1
TATTTTTTTATTTATAAAAAAAATATACTCCTCTC	1	254	0
ATTTTTTTTATAAATAAAAAAATAATTATATAGAA	1	265	1
CAAGAGTGCTTTGAAAATGATAAAAAACCACTATA	2	25	1
AGAAGAATAGTAGAAAAAAAGAACAATAACGAAAA	2	143	0
AAATGAATCTTAGAGATAAAGAAGAATAGTAGAAA	2	162	0
GGCTTCACTCTTGAGAAAAACAAGAGCATAAGGTA	2	224	1
TTATATATTTTTAAAAATAAAAATAACTAATTTAA	6	38	0
TTTTTAAAAATATATAAAAACAAAAAAGCTATTTT	6	56	1
          *  * ***** ** *
MAP Score: 10.5625

Motif 2
CGGCCATTTCAAAAACCCTCTCTCTAAATAT	0	68	1
GCGAAGTAGAACAAAGCTCATCTGTGAGAAA	0	197	1
AGAAAAATTAAAGAAGCCTATCCTTAAGCTC	0	223	1
TTGTCAAAACAAAAATCCTTTTA        	1	2	0
TGGTCCTTAAACAAAACTCCTAACGCCAAGA	1	55	0
GCATAAAAAGACGAACCCCCTAACATAGGGG	1	186	1
CCAATCTTTTTAGAACCCCCTATGTTAGGGG	1	202	0
TGAAAATGATAAAAAACCACTATAATCGATT	2	36	1
TTTTTATAGTAAGAACCTTATAATAATTTCC	4	34	1
ACATTTTCTAAGAAAACCTCTTCCCCATATA	4	118	1
         TAAGAATCTTATTCTATTAAAC	6	1	1
TATAAAAACAAAAAAGCTATTTTAAGAGTAA	6	68	1
          ***** *****
MAP Score: 9.50373

Motif 3
CGATACATTTTTCTTAAATCCAAAAAGTTCCATGT	1	122	0
ATTTATAATCTTACTAAGAACAAAACGTTTGGGCT	2	193	1
GGCTTCACTCTTGAGAAAAACAAGAGCATAAGGTA	2	224	1
CATTGGTCCTTTAGGAATTTCAAGAGCGCATCATC	0	273	1
ACCTAAAGTATTGCTAAATTCAACAACTTTTCGTT	2	116	1
TAAGGACCATTTCTGATGCACAAGAACTACCCTCT	1	77	1
TTAAACAAAACTCCTAACGCCAAGACAACAAGCTG	1	45	0
TTTTTATATATTTTTAAAAATAAAAATAACTAATT	6	41	0
AAGAATTCCTTCATTATCAACAACAGACAATCACA	4	86	1
TATAATTATTTTTTTATTTATAAAAAAAATATACT	1	260	0
TTTTTAAAAATATATAAAAACAAAAAAGCTATTTT	6	56	1
CTACTATTCTTCTTTATCTCTAAGATTCATTTATA	2	165	1
          TTTTTACTCTTAAAATAGCTTTTTT	6	77	0
CAAGAGTGCTTTGAAAATGATAAAAAACCACTATA	2	25	1
          **  ***   *****
MAP Score: 6.76783

Motif 4
       GATGTTCTTTTAATCCCCCAATATTCTGAAAT	0	3	1
CTTCTGAAGTGTCCTTGAAAACGGCCATTTCAAAAACCC	0	47	1
GATGAGCTTTGTTCTACTTCGCTCATATTTTTATGTAAG	0	180	0
AAGGATTTTTGTTTTGACAAGCACTTCATAATCAGCTTG	1	13	1
ATCAGAAATGGTCCTTAAACAAAACTCCTAACGCCAAGA	1	55	0
TAGGGGGTTCGTCTTTTTATGCCTCTACTGTGTACATTT	1	169	0
ATCGATTGAAGTTTTCCCTACCTAATACTTTCTTCATAT	2	60	1
TTTCGTTATTGTTCTTTTTTTCTACTATTCTTCTTTATC	2	144	1
TCCGAATATAGTCCTCTTAATCGAACCTTGGCAACAGC 	2	272	1
TAAGAATCTTATTCTATTAAACGTTTAATTAAATTAGTT	6	10	1
          *****   *  *   ** *
MAP Score: 5.3992

Motif 5
        GATGTTCTTTTAATCCCCCAAT	0	2	1
ACTTCGCTCATATTTTTATGTAAGATTCCC	0	174	0
TGCGATACATTTTTCTTAAATCCAAAAAGT	1	129	0
AGGGGGTTCGTCTTTTTATGCCTCTACTGT	1	177	0
ATCCCCCCAATCTTTTTAGAACCCCCTATG	1	209	0
AGGAGTATATTTTTTTTATAAATAAAAAAA	1	257	1
CCTAATACTTTCTTCATATAGAACCATCTT	2	80	1
TTTTCGTTATTGTTCTTTTTTTCTACTATT	2	143	1
AACATTTAAGTCTTTTTATAGTAAGAACCT	4	22	1
ATGAAGGAATTCTTTTAAGAAAGACGGTCG	4	70	0
GACAATCACATTTTCTAAGAAAACCTCTTC	4	111	1
TATAGATTCCTTTTCATAGAGTTGCTTTAT	4	164	1
TTAAATTAGTTATTTTTATTTTTAAAAATA	6	38	1
ATAGCTTTTTTGTTTTTATATATTTTTAAA	6	58	0
ACAAAAAAGCTATTTTAAGAGTAAAAA   	6	75	1
          **********
MAP Score: 3.26686

Motif 6
AAGCTGATTATGAAGTGCTTGTCAAAACAAAAATCCTTTTA    	1	6	0
CTTGTGCATCAGAAATGGTCCTTAAACAAAACTCCTAACGCCAAG	1	56	0
ATGTACACAGTAGAGGCATAAAAAGACGAACCCCCTAACATAGGG	1	171	1
TAATTATTTTTTTATTTATAAAAAAAATATACTCCTCTCTATTCA	1	248	0
TGAAGTGACCTAAAGTATTGCTAAATTCAACAACTTTTCGTTATT	2	109	1
ATCTCTAAGATTCATTTATAATCTTACTAAGAACAAAACGTTTGG	2	180	1
ACGTTTGGGCTTCACTCTTGAGAAAAACAAGAGCATAAGGTAATT	2	217	1
CAATAAAACATTTAAGTCTTTTTATAGTAAGAACCTTATAATAAT	4	16	1
CCGTCTTTCTTAAAAGAATTCCTTCATTATCAACAACAGACAATC	4	73	1
ACTAATTTAATTAAACGTTTAATAGAATAAGATTCTTA       	6	3	0
TTTGTTTTTATATATTTTTAAAAATAAAAATAACTAATTTAATTA	6	35	0
          *  *    *    * *  ** * **
MAP Score: 0.772166

Motif 7
AGCTCATCTGTGAGAAAAATTAAAGAAGCCTAT	0	211	1
TTTTTGGATTTAAGAAAAATGTATCGCACTAAT	1	131	1
CAGTAGAGGCATAAAAAGACGAACCCCCTAACA	1	178	1
TTTTTATTTATAAAAAAAATATACTCCTCTCTA	1	252	0
TTTTTTTTATAAATAAAAAAATAATTATATAGA	1	266	1
AAGAGTGCTTTGAAAATGATAAAAAACCACTAT	2	26	1
AGAATAGTAGAAAAAAAGAACAATAACGAAAAG	2	142	0
GGTTCTTACTATAAAAAGACTTAAATGTTTTAT	4	18	0
TTTTTAAAAATAAAAATAACTAATTTAATTAAA	6	33	0
ATTTTTATTTTTAAAAATATATAAAAACAAAAA	6	49	1
          * *******  **
MAP Score: 0.430466