AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons015_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242530
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rpoD	148	RNA Polymerase Sigma-66
#1	CT616	300	hypothetical protein
#2	ctc	300	General Stress Protein
#3	rs6	137	S6 Ribosomal Protein
#4	ychB	63	Predicted Kinase
#5	pssA	300	CDP-diacylglycerol-serine-O-phosphatidyltransferase
#6	mesJ	97	PP-loop superfamily ATPase
#7	ftsH	160	ATP-dependent zinc protease

Motif 1
  GGATAAGTAGAAAAGACGGGAGGGGTTT	0	8	1
GATTTTTAGATAAAAAAAAGCCTGTTGATC	0	54	0
TTTATCTTAAGAAAAACAAGAAATCTAGGG	0	83	0
TTAAAACTAAGGAAAAATCGGCCTAGAAAG	0	119	0
GACCGACACAAAAACAGAAGTGTCGGCAGT	1	18	1
TAAAATAGAAAGAAAAATAGGATAGATAAA	1	120	1
CCAAAATTCAAAAAAACAATGATCAATCCC	1	234	1
GACCTAAGGGGGAATAAAAGACAACTCTGG	2	30	0
GCCATCTAAGGGAACAGAAGGCTTGATAAT	2	107	1
TCCGGTTGAGGGAAAAGAAGCCCTTAAGGC	2	236	1
GTTCACTTTTTGAAAAAAAGTTACTGAAAA	3	27	1
GAGGTGGGGAAGAAAAGAATCTCTTCCCCC	4	24	0
AATTAAAAAATAAAAAAAAGAGGTGGGGAA	4	43	0
ACTTGCTCAGGGAAAACACGCAATAACCAT	5	31	1
ATTCAAGCCATAAAAAGAAGCTTCTCAACA	5	220	1
ATTGCTGAAAGAAAAACACTTCTTGTTTTT	7	45	1
TTATAGAGATAAAAAACAAGAAGTGTTTTT	7	56	0
          **********
MAP Score: 16.692

Motif 2
ATCCCTAGATTTCTTGTTTTTCTTAAGATAAA	0	81	1
TCTTTCTATTTTATTGTCTTTTCACCTAAAAT	1	101	0
TTATCTATCCTATTTTTCTTTCTATTTTATTG	1	117	0
TTGGGATTGATCATTGTTTTTTTGAATTTTGG	1	234	0
TTCCACCCCAGAGTTGTCTTTTATTCCCCCTT	2	23	1
TTATCGAAACTGATTATTTTTCAGTAACTTTT	3	42	0
        ACTTTTTGTTTGTTGGGGGAAGAG	4	2	1
GGGGAAGAGATTCTTTTCTTCCCCACCTCTTT	4	25	1
CCACCTCTTTTTTTTATTTTTTAATT      	4	47	1
GGGCTTAGTTTATTTTTTTGTTGAGAAGCTTC	5	236	0
AACGTTCAACTGATTTTCTATTACGGAATCAC	6	11	0
AAACAAGAAGTGTTTTTCTTTCAGCAATCTGC	7	41	0
AGAAAAACACTTCTTGTTTTTTATCTCTATAA	7	54	1
ATATATTGAATAATTATCTGCCTGTTTGATTA	7	121	1
          *  *********
MAP Score: 12.8639

Motif 3
        GGATAAGTAGAAAAGACGGGAGG	0	2	1
GGATTTTTAGATAAAAAAAAGCCTGTTGATC	0	54	0
TATCTTAAGAAAAACAAGAAATCTAGGGATT	0	80	0
AGACCGACACAAAAACAGAAGTGTCGGCAGT	1	17	1
AGACAATAAAATAGAAAGAAAAATAGGATAG	1	114	1
AGGCTTGATAATAATCAGAGGCTGCAAGTAC	2	125	1
AAAATGGCACATACGAAGAAATCCTCTCCAA	2	172	0
GCTTCTTCCAATAACTAGAGATAGCTACTCT	3	92	0
TTAAAAAATAAAAAAAAGAGGTGGGGAAGAA	4	40	0
AATTCAAGCCATAAAAAGAAGCTTCTCAACA	5	219	1
GCTTCTCAACAAAAAAATAAACTAAGCCCCA	5	239	1
ATAGAGATAAAAAACAAGAAGTGTTTTTCTT	7	53	0
TTTTATCTCTATAATTAGAGGTTTATAAACA	7	72	1
GTTTATAAACAAAATAATAAAATATTTTGAT	7	92	1
          **** ******
MAP Score: 12.5525

Motif 4
AGAAAAGACGGGAGGGGTTTTTCTAGGCCTAA	0	18	1
AACAAGAAATCTAGGGATTTTTAGATAAAAAA	0	67	0
TCCTATTCAATAAGAGATTCACATTAAACCAG	2	59	0
TTATTGAATAGGAGAGATTTTCGATTGGGGCC	2	78	1
ACGCTTGCTTGGAGAGGATTTCTTCGTATGTG	2	164	1
TGAATGGCCTTAAGGGCTTCTTTTCCCTCAAC	2	240	0
CGATAACATGGAAGCGCTTCTTATAGAGTAGC	3	68	1
TTTGTTGGGGGAAGAGATTCTTTTCTTCCCCA	4	18	1
TAAAAAACAAGAAGTGTTTTTCTTTCAGCAAT	7	45	0
ATCTCTATAATTAGAGGTTTATAAACAAAATA	7	76	1
GATTAGCATTGTAGTGAGTTTT          	7	148	1
          **** * *****
MAP Score: 7.73801

Motif 5
TTGATCATTGTTTTTTTGAATTTTGGAATATCAACTGTTT	1	220	0
GATTTTCGATTGGGGCCATCTAAGGGAACAGAAGGCTTGA	2	93	1
CGTAGGACCGTTCATCCGGTTGAGGGAAAAGAAGCCCTTA	2	222	1
AAAGGCCTTTTAGCTCAAGGTAATGGAGAATAGCATTTT 	2	271	1
ATAGAGTAGCTATCTCTAGTTATTGGAAGAAGCAAGGTCA	3	90	1
       ACTTTTTGTTTGTTGGGGGAAGAGATTCTTTTC	4	3	1
CTCTCTATCATTTCACTTGCTCAGGGAAAACACGCAATAA	5	17	1
CCCTAGTGGGTTCAGCAGATTGCTGAAAGAAAAACACTTC	7	27	1
          *    *  * *  ***** *
MAP Score: 4.19421

Motif 6
ATCAACAGGCTTTTTTTTATCTAAAAATCCCT	0	55	1
TCCCTAGATTTCTTGTTTTTCTTAAGATAAAC	0	82	1
TCTATCCTATTTTTCTTTCTATTTTATTGTCT	1	114	0
CCCCCTCCTTTATTTTATCTATCCTATTTTTC	1	131	0
CTTCCCCACCTCTTTTTTTTATTTTTTAATT 	4	42	1
ACAGCGCATATTTTTTACATCTTTCTTTGTGA	5	123	0
AAACACTTCTTGTTTTTTATCTCTATAATTAG	7	58	1
AATATTTTATTATTTTGTTTATAAACCTCTAA	7	86	0
          * ****** ***
MAP Score: 2.63287

Motif 7
ACGGGAGGGGTTTTTCTAGGCCTAAATCTGATCAA	0	25	1
GATCAACAGGCTTTTTTTTATCTAAAAATCCCTAG	0	54	1
AGATTTCTTGTTTTTCTTAAGATAAACTGTCACTT	0	87	1
ATCATTGTTTTTTTGAATTTTGGAATATCAACTGT	1	222	0
CCCCACCTCTTTTTTTTATTTTTTAATT       	4	45	1
AGGAGATGTATATTTGTTTGCATAAATGCAAATTC	5	189	1
GAGAAGCTTCTTTTTATGGCTTGAATTTGCATTTA	5	211	0
GCTTAGTTTATTTTTTTGTTGAGAAGCTTCTTTTT	5	231	0
ATGCGCATAGTTTTGTTAGCTAAAACGTTCAACTG	6	31	0
ATTTACACAATTTTTCTATGCGCATAGTTTTGTTA	6	48	0
ACAAGAAGTGTTTTTCTTTCAGCAATCTGCTGAAC	7	36	0
CACTTCTTGTTTTTTATCTCTATAATTAGAGGTTT	7	61	1
TAATAAAATATTTTGATATATTGAATAATTATCTG	7	106	1
          ***** * *   ***
MAP Score: 1.95399