AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons015_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242507
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rpoD	148	RNA Polymerase Sigma-66
#1	ctc	300	General Stress Protein
#2	rs6	137	S6 Ribosomal Protein
#3	ychB	63	Predicted Kinase
#4	pssA	300	CDP-diacylglycerol-serine-O-phosphatidyltransferase
#5	mesJ	97	PP-loop superfamily ATPase
#6	ftsH	160	ATP-dependent zinc protease

Motif 1
  GGATAAGTAGAAAAGACGGGAGGGGTTT	0	8	1
GATTTTTAGATAAAAAAAAGCCTGTTGATC	0	54	0
TTTATCTTAAGAAAAACAAGAAATCTAGGG	0	83	0
TTAAAACTAAGGAAAAATCGGCCTAGAAAG	0	119	0
GACCTAAGGGGGAATAAAAGACAACTCTGG	1	30	0
GCCATCTAAGGGAACAGAAGGCTTGATAAT	1	107	1
TCCGGTTGAGGGAAAAGAAGCCCTTAAGGC	1	236	1
GTTCACTTTTTGAAAAAAAGTTACTGAAAA	2	27	1
AAAGAGGTGGGGAAGAAAAGAATCTCTTCC	3	27	0
AATTAAAAAATAAAAAAAAGAGGTGGGGAA	3	43	0
ACTTGCTCAGGGAAAACACGCAATAACCAT	4	31	1
ATTCAAGCCATAAAAAGAAGCTTCTCAACA	4	220	1
TTATAGAGATAAAAAACAAGAAGTGTTTTT	6	56	0
          **********
MAP Score: 16.9874

Motif 2
AATCTGATCAACAGGCTTTTTTTTATCTAAAAAT	0	49	1
AAATCCCTAGATTTCTTGTTTTTCTTAAGATAAA	0	79	1
GCTTGCTTGGAGAGGATTTCTTCGTATGTGCCAT	1	166	1
AATGGCCTTAAGGGCTTCTTTTCCCTCAACCGGA	1	236	0
ATTATTTTTCAGTAACTTTTTTTCAAAAAGTGAA	2	28	0
TGTTATCGAAACTGATTATTTTTCAGTAACTTTT	2	42	0
TGTTGGGGGAAGAGATTCTTTTCTTCCCCACCTC	3	20	1
AGTTATGGTTATTGCGTGTTTTCCCTGAGCAAGT	4	31	0
TATGTTACACAGAACATGTTTTCGGCACTACACA	4	79	0
AGGACTAAACAGCGCATATTTTTTACATCTTTCT	4	129	0
AGTGGGGCTTAGTTTATTTTTTTGTTGAGAAGCT	4	238	0
AAAAACAAGAAGTGTTTTTCTTTCAGCAATCTGC	6	41	0
          ** *  * ******
MAP Score: 11.6942

Motif 3
GATCAGATTTAGGCCTAGAAAAACCCCTCCCG	0	26	0
AAGGAAAAATCGGCCTAGAAAGTGACAGTTTA	0	109	0
AGACCTAAGGGGGAATAAAAGACAACTCTGGG	1	29	0
GGCCATCTAAGGGAACAGAAGGCTTGATAATA	1	106	1
TATACCAGACGGCCTTAAAATGGCACATACGA	1	187	0
ATCCGGTTGAGGGAAAAGAAGCCCTTAAGGCC	1	235	1
AAGCCCTTAAGGCCATTCAAAGGCCTTTTAGC	1	253	1
AAAAGAGGTGGGGAAGAAAAGAATCTCTTCCC	3	26	0
CACTTGCTCAGGGAAAACACGCAATAACCATA	4	30	1
ACATGTTTTCGGCACTACACAGAAAACCCACA	4	68	0
TAGTGCCAAAAGGACTAAACAGCGCATATTTT	4	141	0
TAGTCCTTTTGGCACTAGAAAGTTCCAAGTCA	4	156	1
TGCAAATTCAAGCCATAAAAAGAAGCTTCTCA	4	215	1
CCACTAGGGCAGCCCCAAAAACACTA      	6	4	0
          ***** * ****
MAP Score: 6.5605

Motif 4
TAGAAAAGACGGGAGGGGTTTTTCTAGGCCTAAAT	0	17	1
TAAATCTGATCAACAGGCTTTTTTTTATCTAAAAA	0	47	1
TTATTGAATAGGAGAGATTTTCGATTGGGGCCATC	1	78	1
ACGCTTGCTTGGAGAGGATTTCTTCGTATGTGCCA	1	164	1
ATGGCCTTAAGGGCTTCTTTTCCCTCAACCGGATG	1	234	0
GTTGGGGGAAGAGATTCTTTTCTTCCCCACCTCTT	3	21	1
CTTTTCTTCCCCACCTCTTTTTTTTATTTTTTAAT	3	37	1
CCATAACTATCTGTGGGTTTTCTGTGTAGTGCCGA	4	57	1
ATGTTACACAGAACATGTTTTCGGCACTACACAGA	4	77	0
GGACTAAACAGCGCATATTTTTTACATCTTTCTTT	4	127	0
TTTTTGTTGAGAAGCTTCTTTTTATGGCTTGAATT	4	219	0
GAAATCAGTGGGGCTTAGTTTATTTTTTTGTTGAG	4	243	0
CTAAAACGTTCAACTGATTTTCTATTACGGAATCA	5	12	0
ATTTTTCTATGCGCATAGTTTTGTTAGCTAAAACG	5	39	0
TAAAAAACAAGAAGTGTTTTTCTTTCAGCAATCTG	6	42	0
          * ** *  ***** *
MAP Score: 5.98085

Motif 5
ATCAACAGGCTTTTTTTTATCTAAAAATCC	0	55	1
TCCCTAGATTTCTTGTTTTTCTTAAGATAA	0	82	1
       ACTTTTTGTTTGTTGGGGGAAGA	3	3	1
CTTCCCCACCTCTTTTTTTTATTTTTTAAT	3	42	1
GTTGAGAAGCTTCTTTTTATGGCTTGAATT	4	219	0
GGGGCTTAGTTTATTTTTTTGTTGAGAAGC	4	239	0
GAAAAACACTTCTTGTTTTTTATCTCTATA	6	55	1
TATTTTATTATTTTGTTTATAAACCTCTAA	6	86	0
          **********
MAP Score: 5.97934

Motif 6
ACGGGAGGGGTTTTTCTAGGCCTAAATCTG	0	25	1
TCAACAGGCTTTTTTTTATCTAAAAATCCC	0	56	1
ATAAACTGTCACTTTCTAGGCCGATTTTTC	0	108	1
TTATTATCAAGCCTTCTGTTCCCTTAGATG	1	109	0
TTTTTCAGTAACTTTTTTTCAAAAAGTGAA	2	28	0
          ACTTTTTGTTTGTTGGGGGA	3	0	1
CTTCCCCACCTCTTTTTTTTATTTTTTAAT	3	42	1
AATAACCATAACTATCTGTGGGTTTTCTGT	4	52	1
CTATCTGTGGGTTTTCTGTGTAGTGCCGAA	4	63	1
ATTTTTTACATCTTTCTTTGTGAAGCCTAA	4	116	0
CGCTGTTTAGTCCTTTTGGCACTAGAAAGT	4	149	1
TTGACTTGGAACTTTCTAGTGCCAAAAGGA	4	159	0
TTGAGAAGCTTCTTTTTATGGCTTGAATTT	4	218	0
GCTTAGTTTATTTTTTTGTTGAGAAGCTTC	4	236	0
CGTTCAACTGATTTTCTATTACGGAATCAC	5	11	0
ATTTACACAATTTTTCTATGCGCATAGTTT	5	53	0
ACAAGAAGTGTTTTTCTTTCAGCAATCTGC	6	41	0
AAAGAAAAACACTTCTTGTTTTTTATCTCT	6	52	1
          **********
MAP Score: 4.18763

Motif 7
GATTTTCGATTGGGGCCATCTAAGGGAACAGAAGGCTTGATA	1	93	1
CGTAGGACCGTTCATCCGGTTGAGGGAAAAGAAGCCCTTAAG	1	222	1
AAAGGCCTTTTAGCTCAAGGTAATGGAGAATAGCATTTT   	1	271	1
GACGGGGATTTACTGTTCACTTTTTGAAAAAAAGTTACTGAA	2	13	1
ATAGAGTAGCTATCTCTAGTTATTGGAAGAAGCAAGGTCAAT	2	90	1
       ACTTTTTGTTTGTTGGGGGAAGAGATTCTTTTCTT	3	3	1
CTCTCTATCATTTCACTTGCTCAGGGAAAACACGCAATAACC	4	17	1
CCCTAGTGGGTTCAGCAGATTGCTGAAAGAAAAACACTTCTT	6	27	1
          *    *    *  ***** * *
MAP Score: 4.15503

Motif 8
TCTAGGGATTTTTAGATAAAAAAAAGCCTGT	0	59	0
GACAGTTTATCTTAAGAAAAACAAGAAATCT	0	87	0
CAAATTAAAACTAAGGAAAAATCGGCCTAGA	0	122	0
AAAGACAACTCTGGGGTGGAAGGATTCGAAC	1	13	0
TAAACCAGACCTAAGGGGGAATAAAAGACAA	1	36	0
TTGGGGCCATCTAAGGGAACAGAAGGCTTGA	1	102	1
GTTCATCCGGTTGAGGGAAAAGAAGCCCTTA	1	231	1
CTCCATTACCTTGAGCTAAAAGGCCTTTGAA	1	268	0
CTGTTCACTTTTTGAAAAAAAGTTACTGAAA	2	25	1
AAAAAAAGAGGTGGGGAAGAAAAGAATCTCT	3	30	0
ATTTCACTTGCTCAGGGAAAACACGCAATAA	4	26	1
AAAGAAGCTTCTCAACAAAAAAATAAACTAA	4	233	1
TCCGCGATTCCTGAGGAAGAT          	4	289	1
GCATAGTTTTGTTAGCTAAAACGTTCAACTG	5	31	0
CAGCAGATTGCTGAAAGAAAAACACTTCTTG	6	39	1
          ** ********
MAP Score: 3.46944