AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_profile002_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238838
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yjjK	54	ABC Transporter Protein ATPase
#1	xerC	84	Integrase/recombinase
#2	atsA	154	Sulphohydrolase/Glycosulfatase
#3	kdsB	175	deoxyoctulonosic Acid Synthetase
#4	yaeS	300	YaeS family hypothetical protein
#5	ndk	71	Nucleoside-2-P Kinase
#6	ruvC	142	Crossover Junction Endonuclease
#7	kdsA	300	KDO Synthetase
#8	thdF	150	Thiophene/Furan Oxidation Protein
#9	pnp	40	Polyribonucleotide Nucleotidyltransferase
#10	rs15	247	S15 Ribosomal Protein

Motif 1
TTTACGATCTTTATTGTAAGGTAAAGAGAAGTT 	1	61	1
AATGACAACTTTTTTATCATTTAAAATTTTGTTT	2	62	0
TTCTGTGACTTTTTCTTAAAGTAAATCCTT    	2	134	1
CCCTTCGAGATTTTTATTTTGTAAAATAAAATAC	3	52	1
AATAAAATACTTTTTTTTCAGAAAAATAAAAAAA	3	76	1
AACACATAAGTTTTTGTTAGGTATCTCCTT    	3	155	1
CTCTCAAAAATTTTCTTCTTGAGACACCGATCTG	4	110	1
CTTTGTGATTTTTGTCTTAGGTAAGTGAACGAAT	4	195	1
CGTTTCGAACCTATTTTTAAGAAAGGAGAATTCG	4	224	0
TAAAACGATTTTATTTAAAGGAGATATGTATACA	5	45	1
TAGCAGGAAATTTTTTTCTAGAAACCGAGAATTC	6	42	1
TACTTTGAACTTATTGTCTTTAAAAGATGATCCT	6	103	0
AGAATTGACTTTTTTCTTGGTAGACCTATACTGA	7	99	0
  GACCATCCTTTTTTAGAATAAAGCAACTTTTG	7	278	0
TAATTTCTTTTTATCGTTTCTAGAGGTCTT    	8	6	0
ATTGTTATTTTTTTTGTTTTTAGAACTCATAATG	10	56	0
GGGTAAGACTTTTTTTTCTATAAACAAAGAAAAA	10	149	0
AATGTACACCTTTTGGTAGGGTAAGACTTTTTTT	10	167	0
TTTGCGGCAATTATTTTAAGGAGACATCCG    	10	227	1
          ***** *   ****
MAP Score: 15.1294

Motif 2
GAACAGGGCAAAGCTCTTGTACTCTAAGCAGCACTT	0	12	1
TTTATCATTTAAAATTTTGTTTTTCTTATAACTCCT	2	48	0
TAAGTTAGTTATCTTGTTTTGTTTTTTAGTTTATT 	3	9	0
TTCTGAAAAAAAAGTATTTTATTTTACAAAATAAAA	3	63	0
TAAAACGCAATATTTTTTTTATTTTTCTGAAAAAAA	3	87	0
TACCTAACAAAAACTTATGTGTTTAAGACTACCAGG	3	142	0
         CAACCTAATATTTTCTACTCCTTTGCT	4	1	1
GATGCCTAAGAAGCCCTTGTATTCATTTGAAGTAAG	4	72	1
AGAACTCTCAAAAATTTTCTTCTTGAGACACCGATC	4	106	1
GCTGGGGAAAAATCCTTTGTGATTTTTGTCTTAGGT	4	181	1
CCTTTAAATAAAATCGTTTTATTTTAGGAGGAGTAT	5	30	0
AAATACTTTGAACTTATTGTCTTTAAAAGATGATCC	6	104	0
TTAGAACCAAAAGTTGCTTTATTCTAAAAAAGGATG	7	271	1
ATCTTTTTATAATTTCTTTTTATCGTTTCTAGAGGT	8	13	0
AAAGTTCCTTTAACTTTTCTATTTTT          	8	134	1
AATTCTAAATAATATTATTTATTCCATTATGAGTTC	10	32	1
TGTATATTGTTATTTTTTTTGTTTTTAGAACTCATA	10	59	0
CACAGCCCCTAATTTTTTCTTTGTTTATAGAAAAAA	10	136	1
TTGGTAGGGTAAGACTTTTTTTTCTATAAACAAAGA	10	153	0
          **  * ** * *** *
MAP Score: 12.6247

Motif 3
TCTTTACCTTACAATAAAGATCGTAAAAAG	1	58	0
ATAAATATGAAGACAACAATGCAGGAGTTA	2	26	1
GTTATAAGAAAAACAAAATTTTAAATGATA	2	52	1
AAAAAGTCACAGAATAAACTAAGTGAAATT	2	118	0
       AATAAACTAAAAAACAAAACAAG	3	3	1
TTTATTTTACAAAATAAAAATCTCGAAGGG	3	52	0
TTTATTTTGTAAAATAAAATACTTTTTTTT	3	64	1
TATTTTTCTGAAAAAAAAGTATTTTATTTT	3	74	0
TTTTTTCAGAAAAATAAAAAAAATATTGCG	3	88	1
CGAGCAAAGGAGTAGAAAATATTAGGTTG 	4	9	0
CGGTGTCTCAAGAAGAAAATTTTTGAGAGT	4	109	0
ATCTGCTTAGAGAATAGAATACAGCCTCTC	4	139	1
CACTTACCTAAGACAAAAATCACAAAGGAT	4	192	0
TACTCCTCCTAAAATAAAACGATTTTATTT	5	31	1
CTCGGTTTCTAGAAAAAAATTTCCTGCTAT	6	41	0
AGGTCTACCAAGAAAAAAGTCAATTCTGAC	7	106	1
TCTTTAGGGAACAAGAAAATCTTGTGTCAG	7	131	0
ATAAGATCGGAGAATACAATCCAAGTTGCT	7	230	0
AGAAACGATAAAAAGAAATTATAAAAAGAT	8	19	1
         AAAAATAGAAAAGTTAAAGGA	8	139	0
TGAGTTCTAAAAACAAAAAAAATAACAATA	10	61	1
CTATAAACAAAGAAAAAATTAGGGGCTGTG	10	136	0
CTTTGTTTATAGAAAAAAAAGTCTTACCCT	10	154	1
          **********
MAP Score: 12.3396

Motif 4
TTCTGTGACTTTTTCTTAAAGTAAATCCTT    	2	134	1
AATAAAATACTTTTTTTTCAGAAAAATAAAAAAA	3	76	1
AGCCCTTGTATTCATTTGAAGTAAGAACTCTCAA	4	83	1
TAAGTCACAATTCGTTCTCAGGAACAACGTTTCG	4	251	0
AATAAAATCGTTTTATTTTAGGAGGAGTATAGCA	5	26	0
ATAAAACGATTTTATTTAAAGGAGATATGTATAC	5	44	1
        GATTCCTACGTAGTAAACAGGACTGT	6	2	1
TAGCAGGAAATTTTTTTCTAGAAACCGAGAATTC	6	42	1
CAGAATTGACTTTTTTCTTGGTAGACCTATACTG	7	100	0
CCTAAAGAACTTCTTTCAAAGCTATATAAAAAGC	7	153	1
CAAAAGTTGCTTTATTCTAAAAAAGGATGGTC  	7	278	1
TGTTATTTTTTTTGTTTTTAGAACTCATAATGGA	10	54	0
TAATTTTTTCTTTGTTTATAGAAAAAAAAGTCTT	10	145	1
TTTTGCGGCAATTATTTTAAGGAGACATCCG   	10	226	1
          *** ***  ** **
MAP Score: 10.3175

Motif 5
AAAGCTCTTGTACTCTAAGCAGCACTTTGTTAT	0	21	1
 CTCGGAAAGAATAGTAAGAAGCTAGCCTTCCT	1	9	1
TTACAATAAAGATCGTAAAAAGACTTCCTCTTA	1	47	0
ATCTTTATTGTAAGGTAAAGAGAAGTT      	1	67	1
GCAGGAGTTATAAGAAAAACAAAATTTTAAATG	2	46	1
CAAAATTTTAAATGATAAAAAAGTTGTCATTCA	2	65	1
   AAGGATTTACTTTAAGAAAAAGTCACAGAA	2	134	0
        AATAAACTAAAAAACAAAACAAGAT	3	2	1
TTTTTTTCAGAAAAATAAAAAAAATATTGCGTT	3	87	1
AAAACGATTTTATTTAAAGGAGATATGTATACA	5	46	1
TTTTATAGGTAAAATTAAGGAGCAACTTGGATT	7	210	1
AAAGTTGCTTTATTCTAAAAAAGGATGGTC   	7	280	1
GACCTCTAGAAACGATAAAAAGAAATTATAAAA	8	12	1
GATAAAAAGAAATTATAAAAAGATTAATGAAAA	8	25	1
TACCAAGTTTTAGATTAAAGAGGTGAAAGGAGT	8	92	0
AAAAATAGAAAAGTTAAAGGAACTTTCGGATAG	8	127	0
ATGAGTTCTAAAAACAAAAAAAATAACAATATA	10	60	1
TTTTTTTCTATAAACAAAGAAAAAATTAGGGGC	10	140	0
TTGCGGCAATTATTTTAAGGAGACATCCG    	10	228	1
          **   ********
MAP Score: 10.0234

Motif 6
AAGAAGCTAGCCTTCCTAAAGCTAAGAGGAA	1	25	1
TTCTGTGACTTTTTCTTAAAGTAAATCCTT 	2	134	1
TTTTTTTTATTTTTCTGAAAAAAAAGTATTT	3	80	0
AGATTAGGAGGATGCCTAAGAAGCCCTTGTA	4	62	1
AATTCGTTCACTTACCTAAGACAAAAATCAC	4	199	0
ACGAATTCTCCTTTCTTAAAAATAGGTTCGA	4	223	1
         ACTTTCCTAAAGATCATGCTAT	5	1	1
AGATTTTCTTGTTCCCTAAAGAACTTCTTTC	7	139	1
ACTTGGTATTCTATCCGAAAGTTCCTTTAAC	8	117	1
AAAGTCTTACCCTACCAAAAGGTGTACATTA	10	171	1
    CGGATGTCTCCTTAAAATAATTGCCGC	10	230	0
          *** *******
MAP Score: 1.50763