AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile007_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243532
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rpiA	94	Ribose-5-P Isomerase A
#1	CT214	300	hypothetical protein
#2	ribC	300	Riboflavin Synthase
#3	exbB	152	polysaccharide transporter
#4	tyrP_2	181	Tyrosine Transport
#5	pssA	300	CDP-diacylglycerol-serine-O-phosphatidyltransferase

Motif 1
TCTAACAAGGGCTTCTATTCCTCAAACAGTAATCCT	0	48	0
GCCCTTGTTAGATTCTTTCCTTTGAGAGGTTT    	0	72	1
TTTATCTTGAGGTTTTCTCCTACGAAATAAATGTTT	1	116	0
GATTTGTGGTGATTTTTTTTCAAAAGTCGCCTAATA	2	29	1
CAAGACACAGGATTTTATCCATTAAAATAAAAACCG	2	88	0
TCTAAGAAGAGGTTCTTTTCAACACAAGACACAGGA	2	112	0
CAGAAGAGTTGTTTTTGTTTTTGCAATTCATTACAT	3	50	1
AAAGGATCTTGGTTCTATACAAGAAATTTGTTAGGA	3	91	1
TTTGCTAGTTGTTTTTCTCCATATAGTATAGATTGG	4	97	1
GCTTGAATTTGCATTTATGCAAACAAATATACATCT	5	192	0
ATAAAAAGAAGCTTCTCAACAAAAAAATAAACTAAG	5	229	1
          * **** * * *  **
MAP Score: 11.6883

Motif 2
AGCCCTTGTTAGATTCTTTCCTTTGAGAGGTTT 	0	71	1
GAGAGTGTGTTGCGCTTTTTTGGGTTTTCACCAT	1	30	0
GAAAAATCGCAGAGTCTTTCATTTTCTTTACCTC	1	193	0
TTGTGATTTGTGGTGATTTTTTTTCAAAAGTCGC	2	25	1
GATAAAATCCTGTGTCTTGTGTTGAAAAGAACCT	2	105	1
AGATCCGGAGAGGGCTTTTTCGTGTATCTAGTTT	2	220	1
TAAACCGGAGAGAGTGTTGTGTTT          	3	0	0
ACAACAGAAGAGTTGTTTTTGTTTTTGCAATTCA	3	46	1
TATAGAACCAAGATCCTTTTTGGTATGTAATGAA	3	76	0
CGCGACTGTTTGCTAGTTGTTTTTCTCCATATAG	4	89	1
CAGATAGTTATGGTTATTGCGTGTTTTCCCTGAG	5	36	0
CATAACTATCTGTGGGTTTTCTGTGTAGTGCCGA	5	58	1
AGGACTAAACAGCGCATATTTTTTACATCTTTCT	5	129	0
TTTGTTGAGAAGCTTCTTTTTATGGCTTGAATTT	5	218	0
AGTGGGGCTTAGTTTATTTTTTTGTTGAGAAGCT	5	238	0
          ** *  **** ***
MAP Score: 9.61047

Motif 3
TAACAAGGGCTTCTATTCCTCAAACAGTAATCCT	0	48	0
    AAACCTCTCAAAGGAAAGAATCTAACAAGG	0	74	0
AAACATTTATTTCGTAGGAGAAAACCTCAAGATA	1	116	1
AGAATAAAAATTAAAAAGAGAAAATAGTTTTT  	1	278	1
CGGTTTTTATTTTAATGGATAAAATCCTGTGTCT	2	88	1
AGAGGTTCTTTTCAACACAAGACACAGGATTTTA	2	107	0
CAGCGGTTACTTATAATCAAAAAATAATTATACT	2	174	0
TCTTGAAAAACTAGATACACGAAAAAGCCCTCTC	2	227	0
TCTAGTTTTTCAAGATTGCTAAAAAGTATTGTTG	2	246	1
TTGCAATTCATTACATACCAAAAAGGATCTTGGT	3	70	1
AGGATCTTGGTTCTATACAAGAAATTTGTTAGGA	3	93	1
CCAATCTATACTATATGGAGAAAAACAACTAGCA	4	99	0
AAAGATTCCCCTATCAACATGAAAAAACAGGGGG	4	151	1
ATGTTTTCGGCACTACACAGAAAACCCACAGATA	5	64	0
ACTTGGAACTTTCTAGTGCCAAAAGGACTAAACA	5	152	0
TAAATGCAAATTCAAGCCATAAAAAGAAGCTTCT	5	211	1
AAAAAGAAGCTTCTCAACAAAAAAATAAACTAAG	5	231	1
          *** *  ** ****
MAP Score: 9.26915

Motif 4
GTGTGTTGCGCTTTTTTGGGTTTTCACCATATTTA	1	25	0
AAAGATCGTTTATCTTGAGGTTTTCTCCTACGAAA	1	125	0
TCGCAGAGTCTTTCATTTTCTTTACCTCACCTTCT	1	186	0
AAATGAAAGACTCTGCGATTTTTCCCCGTTCTAAA	1	203	1
TATTTTCTCTTTTTAATTTTTATTCTGCACACATT	1	269	0
TTGTGATTTGTGGTGATTTTTTTTCAAAAGTCGCC	2	25	1
GGCTTTTTCGTGTATCTAGTTTTTCAAGATTGCTA	2	232	1
ACAGAAGAGTTGTTTTTGTTTTTGCAATTCATTAC	3	49	1
GCTTTCATCATTTCGATCTGTTTACAAAAAGCTCG	4	55	0
CGCGACTGTTTGCTAGTTGTTTTTCTCCATATAGT	4	89	1
     CCTCCTCCCCCTGTTTTTTCATGTTGATAG	4	161	0
TAGTTATGGTTATTGCGTGTTTTCCCTGAGCAAGT	5	31	0
TAACCATAACTATCTGTGGGTTTTCTGTGTAGTGC	5	54	1
TCAAAGGAGATGTATATTTGTTTGCATAAATGCAA	5	185	1
          * **  * ***** *
MAP Score: 7.5288

Motif 5
CTTTTTTGGGTTTTCACCATATTTAAAATAGGAGCATCTT	1	10	0
TATAAATCTTTCTTAGCATGCAAACATTTATTTCGTAGGA	1	95	1
TGTGGTGATTTTTTTTCAAAAGTCGCCTAATATCTGCAGG	2	33	1
AGACACAGGATTTTATCCATTAAAATAAAAACCGTGGTAT	2	82	0
AAGAAGAGGTTCTTTTCAACACAAGACACAGGATTTTATC	2	105	0
CGTGTATCTAGTTTTTCAAGATTGCTAAAAAGTATTGTTG	2	240	1
ACTCTCTCCGGTTTAGCAAATCATCAAACAACAGAAGAGT	3	19	1
GTTGTTTTTGTTTTTGCAATTCATTACATACCAAAAAGGA	3	57	1
GGATCTTGGTTCTATACAAGAAATTTGTTAGGATCGTCTA	3	94	1
TGCTAGTTGTTTTTCTCCATATAGTATAGATTGGATCGTA	4	99	1
ATAACCTTAGGCTTCACAAAGAAAGATGTAAAAAATATGC	5	110	1
TGAATTTGCATTTATGCAAACAAATATACATCTCCTTTGA	5	185	0
ATAAAAAGAAGCTTCTCAACAAAAAAATAAACTAAGCCCC	5	229	1
          ****  ***   *  *   *
MAP Score: 6.85502

Motif 6
AACCCAAAAAAGCGCAACACACTCTCCGTCAGAGCGGA	1	38	1
TGAGGTAAAGAAAATGAAAGACTCTGCGATTTTTCCCC	1	192	1
GTGTCTTGTGTTGAAAAGAACCTCTTCTTAGAAAGGTT	2	116	1
ACCTCTTCTTAGAAAGGTTTTCTCTACGGGCGGTCTCG	2	135	1
AACTAGATACACGAAAAAGCCCTCTCCGGATCTGATCA	2	215	0
         AAACACAACACTCTCTCCGGTTTAGCAAA	3	1	1
GAATTGCAAAAACAAAAACAACTCTTCTGTTGTTTGAT	3	41	0
TCAAGCCATAAAAAGAAGCTTCTCAACAAAAAAATAAA	5	222	1
          *  * **    **** **
MAP Score: 6.25413

Motif 7
AAGGGCTTCTATTCCTCAAACAGTAATCCTACA	0	45	0
TCTCAAAGGAAAGAATCTAACAAGGGCTTCTAT	0	66	0
AAATATGGTGAAAACCCAAAAAAGCGCAACACA	1	26	1
TAAAAATTAAAAAGAGAAAATAGTTTTT     	1	282	1
AAATCACCACAAATCACAATCAAGAATTGTGTT	2	11	0
GGTTACTTATAATCAAAAAATAATTATACTCCG	2	171	0
CGGTTTAGCAAATCATCAAACAACAGAAGAGTT	3	27	1
ATGAATTGCAAAAACAAAAACAACTCTTCTGTT	3	48	0
GGAGAAAAACAACTAGCAAACAGTCGCGCTTTC	4	84	0
CCCCTATCAACATGAAAAAACAGGGGGAGGAGG	4	158	1
CTAGTGCCAAAAGGACTAAACAGCGCATATTTT	5	141	0
ATGCAAATTCAAGCCATAAAAAGAAGCTTCTCA	5	214	1
GAAGCTTCTCAACAAAAAAATAAACTAAGCCCC	5	236	1
          **  * *******
MAP Score: 4.78896

Motif 8
TGAGGTAAAGAAAATGAAAGACTCTGCGATT	1	192	1
AATGAATTGCAAAAACAAAAACAACTCTTCT	3	51	0
TTCCCCTATCAACATGAAAAAACAGGGGGAG	4	156	1
  AAACCTCTCAAAGGAAAGAATCTAACAAG	0	75	0
AAAAACTAGATACACGAAAAAGCCCTCTCCG	2	225	0
CTTAGGCTTCACAAAGAAAGATGTAAAAAAT	5	115	1
GTGCAGAATAAAAATTAAAAAGAGAAAATAG	1	274	1
GCGGTTACTTATAATCAAAAAATAATTATAC	2	175	0
TTTTATCCATTAAAATAAAAACCGTGGTATC	2	81	0
AAAGAAGCTTCTCAACAAAAAAATAAACTAA	5	233	1
AACTAAAGACTCCAGGAAAGATCGTTTATCT	1	145	0
AAATATGGTGAAAACCCAAAAAAGCGCAACA	1	26	1
CAATTCATTACATACCAAAAAGGATCTTGGT	3	73	1
CTCAAAGATCTTAACTAAAGACTCCAGGAAA	1	157	0
CACCACAAATCACAATCAAGAATTGTGTTA 	2	9	0
          **** ******
MAP Score: 3.57162

Motif 9
GCCCTTGTTAGATTCTTTCCTTTGAGAGGT	0	72	1
CGCTTTTTTGGGTTTTCACCATATTTAAAA	1	22	0
TTTATCTTGAGGTTTTCTCCTACGAAATAA	1	122	0
AAGACTCTGCGATTTTTCCCCGTTCTAAAG	1	209	1
    AAAAACTATTTTCTCTTTTTAATTTT	1	284	0
TGATTTGTGGTGATTTTTTTTCAAAAGTCG	2	28	1
AAGATACCACGGTTTTTATTTTAATGGATA	2	79	1
ACAAGACACAGGATTTTATCCATTAAAATA	2	95	0
TCTAAGAAGAGGTTCTTTTCAACACAAGAC	2	118	0
TTCTTAGAAAGGTTTTCTCTACGGGCGGTC	2	140	1
ACAGAAGAGTTGTTTTTGTTTTTGCAATTC	3	49	1
ATACCAAAAAGGATCTTGGTTCTATACAAG	3	84	1
GTTTGCTAGTTGTTTTTCTCCATATAGTAT	4	96	1
GGTTATTGCGTGTTTTCCCTGAGCAAGTGA	5	29	0
ACTATCTGTGGGTTTTCTGTGTAGTGCCGA	5	62	1
TAAGCCCCACTGATTTCTGTAATAAATTTC	5	261	1
          **********
MAP Score: 2.65196