AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons031_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243066
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ribC	300	Riboflavin Synthase
#1	pcnB_1	214	PolyA Polymerase
#2	gltX	271	Glutamyl-tRNA Synthetase
#3	clpP_2	166	CLP Protease

Motif 1
GATACACGAAAAAGCCCTCTCCGGATCTGA	0	218	0
CAACAAAAAAAAAGCCCCCCTCCGGAATTC	2	63	0
GAGAACTCTAAAAGCCTTCTTGCTCAAGGA	1	156	1
      AGATAGAGCCTTCTCTGTAAGGGC	2	4	1
TTTTTTTTCAAAAGTCGCCTAATATCTGCA	0	41	1
CGGACCGTTCAAAGCCCTATGTTCCTAAAC	2	162	0
TAGTTTTGTTAAAGTCGCCAAGAATGAATC	2	121	1
GAAGGCTTTTAGAGTTCTCTCCAGGAAAGC	1	145	0
TAAAGATAGAAAAGTTTCCTTTCCTGGGTT	2	243	1
CCTAGAAAAGAAAGACCCCATCTAATTCAA	3	85	0
TATTATAGGAAGAGCTTTCCTGGAGAGAAC	1	132	1
GCTCAAGGACAAAATCCTCCAGACTTTTTA	1	177	1
GGAGGAGGCCCAAGCTCTCCCCTGCTGTGC	2	32	0
          **********
MAP Score: 12.8133

Motif 2
TTATTTTAATGGATAAAATCCTGTGTCTTGTG	0	94	1
TGTCTTGTGTTGAAAAGAACCTCTTCTTAGAA	0	117	1
GACCGCCCGTAGAGAAAACCTTTCTAAGAAGA	0	138	0
GATCAGATCCGGAGAGGGCTTTTTCGTGTATC	0	216	1
        AAGGAGAGAGAGTCATAAAGCTGT	1	2	1
GAGCTTTCCTGGAGAGAACTCTAAAAGCCTTC	1	143	1
TCTTGCTCAAGGACAAAATCCTCCAGACTTTT	1	173	1
          AGATAGAGCCTTCTCTGTAAGG	2	0	1
CCGGAATTCCGGAGGAGGCCCAAGCTCTCCCC	2	40	0
CCGGAATTCCGGAGGGGGGCTTTTTTTTTGTT	2	60	1
TTTTTTTTGTTGAAAAAGAGCTCCGAAAAACT	2	81	1
CTGATTCATAGGACAGGAACCCGGGACGGGGT	2	201	1
CAGGAACCCGGGACGGGGTGTTCATTTCATAA	2	214	1
TACTAACCCAGGAAAGGAAACTTTTCTATCTT	2	245	0
ATTTTGAATTAGATGGGGTCTTTCTTTTCTAG	3	82	1
CCAAATGATTTGAGAGGAAGCACACAT     	3	149	1
          *** **** ***
MAP Score: 12.4502

Motif 3
CCTAATATCTGCAGGACGCTCAAGATACCAC	0	58	1
GTCTTGTGTTGAAAAGAACCTCTTCTTAGAA	0	118	1
GACCGCCCGTAGAGAAAACCTTTCTAAGAAG	0	139	0
GATCAGATCCGGAGAGGGCTTTTTCGTGTAT	0	216	1
        AAGGAGAGAGAGTCATAAAGCTG	1	2	1
TTTCTATTATAGGAAGAGCTTTCCTGGAGAG	1	128	1
GAGCTTTCCTGGAGAGAACTCTAAAAGCCTT	1	143	1
GTGCCCTTACAGAGAAGGCTCTATCT     	2	5	0
GGGCACAGCAGGGGAGAGCTTGGGCCTCCTC	2	30	1
CCGGAATTCCGGAGGAGGCCCAAGCTCTCCC	2	41	0
CGGAATTCCGGAGGGGGGCTTTTTTTTTGTT	2	61	1
TTTTTTGTTGAAAAAGAGCTCCGAAAAACTC	2	83	1
CTATCTTTATGAAATGAACACCCCGTCCCGG	2	221	0
CTAACCCAGGAAAGGAAACTTTTCTATCTTT	2	244	0
TTTGATCGCAGGAAAACGCTTGACCCAAGAG	3	11	1
AAATGATTTGAGAGGAAGCACACAT      	3	151	1
          ********* *
MAP Score: 7.92719

Motif 4
ATTGTGATTTGTGGTGATTTTTTTTCAAAAGTCG	0	24	1
ACCTTTCTAAGAAGAGGTTCTTTTCAACACAAGA	0	119	0
GATCAGATCCGGAGAGGGCTTTTTCGTGTATCTA	0	216	1
CGGAATTCCGGAGGGGGGCTTTTTTTTTGTTGAA	2	61	1
AACGAGTTTTTCGGAGCTCTTTTTCAACAAAAAA	2	83	0
AACCCGGGACGGGGTGTTCATTTCATAAAGATAG	2	218	1
AGTGTCTCTTGGGTCAAGCGTTTTCCTGCGATCA	3	13	0
CTTAAACATAGAATTCATCATTTTGATGCGTAGG	3	45	1
TGAATTAGATGGGGTCTTTCTTTTCTAGGGTCAA	3	86	1
          * ** * ** ****
MAP Score: 7.78772

Motif 5
TTGTGGTGATTTTTTTTCAAAAGTCGCCTAATATCTG	0	32	1
ACGGTTTTTATTTTAATGGATAAAATCCTGTGTCTTG	0	87	1
GAAGAGGTTCTTTTCAACACAAGACACAGGATTTTAT	0	106	0
AGAGAAAACCTTTCTAAGAAGAGGTTCTTTTCAACAC	0	123	0
AGAAAGGTTTTCTCTACGGGCGGTCTCGGAGTATAAT	0	145	1
TATAATTATTTTTTGATTATAAGTAACCGCTGTTTGC	0	176	1
TAACCGCTGTTTGCCTTGATCAGATCCGGAGAGGGCT	0	199	1
AGGCACGTCTTTTTGATCATCAACAGCTTTATGACTC	1	19	0
AAAAATTACGTTTACAAGGGCAAAATCACCTATATGT	1	93	0
TAGGAAGAGCTTTCCTGGAGAGAACTCTAAAAGCCTT	1	137	1
GGGGCTTTTTTTTTGTTGAAAAAGAGCTCCGAAAAAC	2	75	1
TTTATGCCTGATTCATAGGACAGGAACCCGGGACGGG	2	194	1
AAAAGTTTCCTTTCCTGGGTTAGTAGCGA        	2	252	1
TGTTTAAGTGTCTCTTGGGTCAAGCGTTTTCCTGCGA	3	16	0
GGGTCTTTCTTTTCTAGGGTCAAGAGTAGCCATAACG	3	97	1
          **** * **  **   *
MAP Score: 6.56245

Motif 6
TTGTGATTTGTGGTGATTTTTTTTCAAAAGT	0	25	1
TGCAGATATTAGGCGACTTTTGAAAAAAAAT	0	40	0
CTTTCTAAGAAGAGGTTCTTTTCAACACAAG	0	120	0
ACCTCTTCTTAGAAAGGTTTTCTCTACGGGC	0	135	1
ATCAGATCCGGAGAGGGCTTTTTCGTGTATC	0	217	1
ATGATCAAAAAGACGTGCCTTATATATGGTC	1	36	1
AGAAACATATAGGTGATTTTGCCCTTGTAAA	1	89	1
TTCTATTATAGGAAGAGCTTTCCTGGAGAGA	1	129	1
TCCTTGAGCAAGAAGGCTTTTAGAGTTCTCT	1	155	0
TAAAAAGTCTGGAGGATTTTGTCCTTGAGCA	1	176	0
GGCACAGCAGGGGAGAGCTTGGGCCTCCTCC	2	31	1
GGAATTCCGGAGGGGGGCTTTTTTTTTGTTG	2	62	1
AAAACTAAAATAACGAGTTTTTCGGAGCTCT	2	97	0
AACCCAGGAAAGGAAACTTTTCTATCTTTAT	2	242	0
TTTGAATTAGATGGGGTCTTTCTTTTCTAGG	3	84	1
ATTTGGTTACAGGTGTGCTTACGTTATGGCT	3	124	0
          *** *******
MAP Score: 4.66457

Motif 7
TTCTTGATTGTGATTTGTGGTGATTTTTTTTCAAA	0	18	1
AAAACCTTTCTAAGAAGAGGTTCTTTTCAACACAA	0	121	0
CTTGATCAGATCCGGAGAGGGCTTTTTCGTGTATC	0	213	1
CCTCCGGAATTCCGGAGGGGGGCTTTTTTTTTGTT	2	57	1
TAACGAGTTTTTCGGAGCTCTTTTTCAACAAAAAA	2	83	0
ATCATTTTGATGCGTAGGTGTATTTTGAATTAGAT	3	61	1
GTATTTTGAATTAGATGGGGTCTTTCTTTTCTAGG	3	80	1
          * ** ** ***  **
MAP Score: 4.39309

Motif 8
GTGGTATCTTGAGCGTCCTGCAGATATTAGGCGA	0	55	0
TTTTCTCTACGGGCGGTCTCGGAGTATAATTATT	0	152	1
ATACACGAAAAAGCCCTCTCCGGATCTGATCAAG	0	213	0
     AGATAGAGCCTTCTCTGTAAGGGCACAGC	2	5	1
GGGAGAGCTTGGGCCTCCTCCGGAATTCCGGAGG	2	41	1
ACAAAAAAAAAGCCCCCCTCCGGAATTCCGGAGG	2	57	0
      ATGTGTGCTTCCTCTCAAATCATTTGGT	3	148	0
          * **  **** ***
MAP Score: 3.54351

Motif 9
ACCTCTTCTTAGAAAGGTTTTCTCTACGGGCGG	0	135	1
GATCAGATCCGGAGAGGGCTTTTTCGTGTATCT	0	216	1
GTCACGACCTAGCAAAGGTATTTAATTGTCT  	0	279	1
TTTCTATTATAGGAAGAGCTTTCCTGGAGAGAA	1	128	1
          AGATAGAGCCTTCTCTGTAAGGG	2	0	1
AGCAGGGGAGAGCTTGGGCCTCCTCCGGAATTC	2	36	1
GGAATTCCGGAGGGGGGCTTTTTTTTTGTTGAA	2	62	1
CAGGAACCCGGGACGGGGTGTTCATTTCATAAA	2	214	1
ATTTTGAATTAGATGGGGTCTTTCTTTTCTAGG	3	82	1
          **  ***** ***
MAP Score: 2.54141