AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons002_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237131
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yaeM	128	CT071 hypothetical protein
#1	yhfO	24	NifS-related aminotransferase
#2	CPn0397	300	PP2C phosphatase family
#3	yaeS	300	YaeS family hypothetical protein
#4	uhpC	243	Hexosphosphate Transport
#5	yfhO_1	28	NifS-related Aminotransferase
#6	CPn0692	300	ABC Transporter
#7	CPn0693	70	TPR Repeats-CT683 hypothetical protein
#8	pbp2	300	PBP2-transglycolase/transpeptidase
#9	rs2	300	S2 Ribosomal Protein
#10	pgmA	155	Phosphoglycerate Mutase
#11	CPn0921	129	snGlycerol-3-P Acyltransferase

Motif 1
AGAAAATTCTTTCTCTTTTCTTCTGGGCTTGA	6	150	1
GAAAAAAGCATTCTCTTTACTATTATCTTGTT	2	61	0
ACTGGTCTACTTTTCTTTGCTTAAAAACTTTT	10	53	1
TAAAGTAGGCTTTTCTTCGCATTTCATCTCAG	4	190	1
AGTGAACGAATTCTCCTTTCTTAAAAATAGGT	3	218	1
CGGAGTATGATTCTCTTTTTCACCTAGTTAAA	0	96	1
TTACAAAAAATTCTTTTTCCCTAAGTAAGGGG	11	102	1
TTTATCAAATTTTTCTTTGTAATTAATGATCA	2	145	1
CTCTCAAAAATTTTCTTCTTGAGACACCGATC	3	110	1
        TTTTCTTTTGGCATGGTTTTCGCT	7	2	1
AATAATTCATTTGTCTTGATGTGATGTGAAGT	9	32	0
GATTCCCTCCTTGTTTTTTCATCCTTGATATG	4	157	1
AGAGGCTGTATTCTATTCTCTAAGCAGATCGG	3	136	0
GACAAAAATTTTTTATTTCCCTAGAATGGCTT	6	54	1
AGTAGAGTGTTTTTCTTGGTTATTTTTAATTA	4	96	0
AATATCGTGCTTCTTTTTATTATTGTATTTAG	8	199	1
TATCTTAGCTTTGTCCTCGTGTAATTTAATAC	6	240	1
TCTTGAGAAATTTTTTTTGTTTATTTTTATTA	8	56	1
AAGAATTGAATTTTCCTGACGAAATCATAATT	2	199	0
TAAGAAGCCCTTGTATTCATTTGAAGTAAGAA	3	78	1
ACCTAATATTTTCTACTCCTTTGCTCGTCATG	3	12	1
TAAAAACTTTTTTTACTTCTATATTTTCTACT	10	74	1
TTCTCAAGTCTTTTTCTCTTGAGAAATTTTTT	8	40	1
          ******** * *
MAP Score: 12.1634

Motif 2
TAATAGTAAAGAGAATGCTTTTTTCATTATTCATCCTT	2	68	1
GATGGCTGGGGAAAAATCCTTTGTGATTTTTGTCTTAG	3	177	1
TCTTAGGTAAGTGAACGAATTCTCCTTTCTTAAAAATA	3	209	1
CGTTGTTCCTGAGAACGAATTGTGACTTACGCCCTAAT	3	256	1
ATAAACTAGGGAAATAGTGTTTTCAATTGAAATTAGAA	6	16	1
GAAATTAGAAGACAAAAATTTTTTATTTCCCTAGAATG	6	44	1
AGGATTTTTAGAAAATTCTTTCTCTTTTCTTCTGGGCT	6	141	1
TTTTTCTCTTGAGAAATTTTTTTTGTTTATTTTTATTA	8	50	1
TTATTATTTAGAACATGATTTTTGGTTTTAATATGTTT	8	82	1
TTGATTGGACTAAAATTAGTTGTATTTTGCGAACTGTA	8	119	1
GAATGCCGTTGTTAACGTATTCTAATTTTGAAATAGAG	9	263	1
TTTCTTTGCTTAAAAACTTTTTTTACTTCTATATTTTC	10	64	1
AGCATAAGCAGAAATCAACTTTTGTCTAGTAGAAAATA	10	95	0
CTTACTTAGGGAAAAAGAATTTTTTGTAAGCACTATGC	11	93	0
          ** **    ****   **
MAP Score: 11.6315

Motif 3
CGAGCAAAGGAGTAGAAAATATTAGGTTG 	3	9	0
CGGTGTCTCAAGAAGAAAATTTTTGAGAGT	3	109	0
ACTTTTGTCTAGTAGAAAATATAGAAGTAA	10	86	0
AACTAGGTGAAAAAGAGAATCATACTCCGC	0	95	0
AAATAGTATCAATAGAGAATTGACAATTCC	0	58	1
ATGATATGAAATTAGAGAATGTCTATAGGG	2	238	1
ACAGGAAGCTATTAGAAAATAGCATAAGTA	9	64	0
TTTCAAGCCCAGAAGAAAAGAGAAAGAATT	6	154	0
CACCGATCTGCTTAGAGAATAGAATACAGC	3	134	1
AGATGAAATGCGAAGAAAAGCCTACTTTAC	4	189	0
AAGATAATAGTAAAGAGAATGCTTTTTTCA	2	64	1
AGTTTTTAAGCAAAGAAAAGTAGACCAGTA	10	52	0
AGTTAGGATTTTTAGAAAATTCTTTCTCTT	6	137	1
TATTTTTAAGAAAGGAGAATTCGTTCACTT	3	217	0
TCTAGATACTTGAGGAAAATTCT       	11	3	0
          **********
MAP Score: 10.595

Motif 4
GTGTTTTCAATTGAAATTAGAAGACAAAAATTTTT	6	32	1
ACCTATTTTTAAGAAAGGAGAATTCGTTCACTTAC	3	215	0
TTGTATTCATTTGAAGTAAGAACTCTCAAAAATTT	3	88	1
AGGATGAATAATGAAAAAAGCATTCTCTTTACTAT	2	70	0
CCGATCTGCTTAGAGAATAGAATACAGCCTCTCCC	3	136	1
TACCTCTATTTCAAAATTAGAATACGTTAACAACG	9	269	0
AGGAAGCTATTAGAAAATAGCATAAGTAAATAATT	9	57	0
TCAAGCCCAGAAGAAAAGAGAAAGAATTTTCTAAA	6	147	0
TTTCACTGAGATGAAATGCGAAGAAAAGCCTACTT	4	192	0
TCTCAACTAAATGAGGAGCGAAAACCATGCCAAAA	7	15	0
TTTCACCTAGTTAAAGGTAGCATGC          	0	113	1
ACCCTTATTGAGGAGGGACGCAACCACTAAGAGCT	2	16	1
CAAAGAAGGCTTGAAAGACGAACCTACCCCTTTCA	6	179	0
TTTAACTAGGTGAAAAAGAGAATCATACTCCGCAA	0	93	0
AATACAATAATAAAAAGAAGCACGATATTTAAGAA	8	193	0
TTAATTAAATAAGAAATACTAAAACAGCGTATTTT	4	68	0
ATAATTAACTTTGGGAGGCGCATGCA         	4	1	0
AAGAATTTTCTAAAAATCCTAACTCCCTTGGAGAT	6	126	0
CATTCTGACATAAAAGCCAGAATTTCAGTCTTGGT	9	233	0
ATGTTAAACTTCGGGAGTAGCACTATAATAGATAG	11	59	1
CCCCTTACTTAGGGAAAAAGAATTTTTTGTAAGCA	11	99	0
          * ****  ****  *
MAP Score: 8.87121

Motif 5
TTGAACCCTTATTGAGGAGGGACGCAACCAC	2	12	1
ACAAGATAATAGTAAAGAGAATGCTTTTTTC	2	62	1
GAGAATGTCTATAGGGGCGGACTCTATTTGT	2	252	1
GCTCGTCATGAGTAAGCCGAGTATACTTAGA	3	34	1
CAGCCATCCCAGTAGGGAGAGGCTGTATTCT	3	154	0
CCTATTTTTAAGAAAGGAGAATTCGTTCACT	3	218	0
AGGATCATTTATTAGGGCGTAAGTCACAATT	3	273	0
  GTTTAGGATTTAGGGGGGGGGATGATCA 	5	8	1
CAAGCCCAGAAGAAAAGAGAAAGAATTTTCT	6	150	0
CTTCTGGGCTTGAAAGGGGTAGGTTCGTCTT	6	169	1
AGGAGCCATTTTTAAGGGGAACT        	8	2	0
TGTGATGTGAAGTAGGGGGGGAATAAAAATT	9	14	0
CGCAAACTGGATTAAGGGGTGTAGTAGTGTA	9	123	0
CCTACTAGAATTTAGGGTGAGAAGCTAAGCA	10	129	0
TTTTTCCCTAAGTAAGGGGAACTT       	11	115	1
          ******* ***
MAP Score: 8.31766

Motif 6
CTTAGCTTTGTCCTCGTGTAATTTAATACGATAAATTCAAGAGTT	6	243	1
TGGTTTTCGCTCCTCATTTAGTTGAGATCAACGAATCATGTGCTG	7	23	1
AAACTTTTTTTACTTCTATATTTTCTACTAGACAAAAGTTGATTT	10	77	1
GTTTTAGTATTTCTTATTTAATTAAAAATAACCAAGAAAAACACT	4	78	1
AGCAAGGCAATACTGGTCTACTTTTCTTTGCTTAAAAACTTTTTT	10	42	1
GTAAAGAGAATGCTTTTTTCATTATTCATCCTTAGGTTAATTGAC	2	73	1
TAATATTTTCTACTCCTTTGCTCGTCATGAGTAAGCCGAGTATAC	3	15	1
AGAAAATTCTTTCTCTTTTCTTCTGGGCTTGAAAGGGGTAGGTTC	6	150	1
TTTGCTAACATTCTTATCTAGATACTTGAGGAAAATTCT      	11	4	0
TTGCGGAGTATGATTCTCTTTTTCACCTAGTTAAAGGTAGCATGC	0	93	1
CCTCACTACCTTCTCAAGTCTTTTTCTCTTGAGAAATTTTTTTTG	8	30	1
TAGCGATAAATTATGATTTCGTCAGGAAAATTCAATTCTTTATAA	2	191	1
TTAAATATCGTGCTTCTTTTTATTATTGTATTTAGCAGACTATGA	8	196	1
AAACCAAAAATCATGTTCTAAATAATAAAAATAAACAAAAAAAAT	8	65	0
GGGCGATTATTTATCAAATTTTTCTTTGTAATTAATGATCATGCG	2	136	1
AGTAGTGTAATAATGCTTTTAACGCAAGCGTGTAATCTACAGGAA	9	87	0
          * *** * *  **          **
MAP Score: 6.90445

Motif 7
TGTCTCAAGAAGAAAATTTTTGAGAGTTCTT	3	105	0
TTTTCTCTTGAGAAATTTTTTTTGTTTATTT	8	51	1
TAGGATTTTTAGAAAATTCTTTCTCTTTTCT	6	140	1
ATTAGAAGACAAAAATTTTTTATTTCCCTAG	6	47	1
TTCTTTGCTTAAAAACTTTTTTTACTTCTAT	10	65	1
TAGTGCTTACAAAAAATTCTTTTTCCCTAAG	11	96	1
CATCTCAGTGAAAAAGATTTTACACATGGAA	4	214	1
          ***** *****
MAP Score: 5.69945

Motif 8
ATGATTCTCTTTTTCACCTAGTTAAAGGTAGCATGC 	0	102	1
        AGTTGAACCCTTATTGAGGAGGGACGCAA	2	2	1
TTTTTCATTATTCATCCTTAGGTTAATTGACCTTTCC	2	87	1
TAATTGACCTTTCCAGCCTAGCTCTAGGGCGATTATT	2	110	1
CCTTTGTGATTTTTGTCTTAGGTAAGTGAACGAATTC	3	194	1
CTCCTTGTTTTTTCATCCTTGATATGGTAAAGTAGGC	4	163	1
TGGCATGGTTTTCGCTCCTCATTTAGTTGAGATCAAC	7	18	1
AAGCCAGAATTTCAGTCTTGGTTGTGTAAAGAAAGCG	9	218	0
AAGTAGACCAGTATTGCCTTGCTTAGGCACAATAGGT	10	28	0
CAAAAAATTCTTTTTCCCTAAGTAAGGGGAACTT   	11	105	1
          **    *** * * ***
MAP Score: 5.49924

Motif 9
GGTTAATTGACCTTTCCAGCCTAGCTCTAG	2	107	1
CCTACTTTACCATATCAAGGATGAAAAAAC	4	169	0
CGAACCTACCCCTTTCAAGCCCAGAAGAAA	6	166	0
GGTAGGTTCGTCTTTCAAGCCTTCTTTGTT	6	186	1
AGAGCTGTAGCCTTCCAAGCTACCGGTGTC	9	170	1
  GTTTACCCCATATCAAGCACCTATTGTG	10	8	1
          **********
MAP Score: 3.64534

Motif 10
CGGAGTATGATTCTCTTTTTCACCTAGTTAAA	0	96	1
GAAAAAAGCATTCTCTTTACTATTATCTTGTT	2	61	0
AGAGAATGCTTTTTTCATTATTCATCCTTAGG	2	77	1
TATCAAATTTTTCTTTGTAATTAATGATCATG	2	147	1
GAAAATTCAATTCTTTATAATAATGATATGAA	2	216	1
TGGGGAAAAATCCTTTGTGATTTTTGTCTTAG	3	183	1
AGTGAACGAATTCTCCTTTCTTAAAAATAGGT	3	218	1
TTTTTCTTGGTTATTTTTAATTAAATAAGAAA	4	87	0
CCCTCCTTGTTTTTTCATCCTTGATATGGTAA	4	161	1
AAGTAGGCTTTTCTTCGCATTTCATCTCAGTG	4	192	1
TTTTAGAAAATTCTTTCTCTTTTCTTCTGGGC	6	146	1
CTTTCAAGCCTTCTTTGTTATACTGAAAAAAT	6	197	1
TCTTGAGAAATTTTTTTTGTTTATTTTTATTA	8	56	1
GAACTGTATCTTCTCTAGATTTTGTTCGATTA	8	149	1
AATATCGTGCTTCTTTTTATTATTGTATTTAG	8	199	1
GAGAGCATAGTTCTCTGTAATTTTCAGACGAG	8	254	1
ACTGGTCTACTTTTCTTTGCTTAAAAACTTTT	10	53	1
TGCTTAAAAACTTTTTTTACTTCTATATTTTC	10	70	1
          ****** * ***
MAP Score: 1.56245