AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile002_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243260
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	mutY	46	A/G-specific Adenine Glycosylase
#1	kdsB	300	CMP-2-keto-3-deoxyoctulosonic acid synthetase
#2	proS	200	Prolyl tRNA Synthetase
#3	yaeS	300	YaeS family
#4	ndk	159	Nucleoside-2-P Kinase
#5	kdsA	300	KDO Synthetase
#6	thdF	266	Thiophene/Furan Oxidation Protein
#7	pnp	28	Polyribonucleotide Nucleotidyltransferase
#8	rs15	156	S15 Ribosomal Protein

Motif 1
CTAGATATTTACAAGCCTTCTCATAGGCTCT	1	45	1
AAGATTATTCACAGAGCTACTAGCTTTCTTA	1	146	0
CTTGATTGTTAACGATCTCCTTGTTAGGATG	1	174	1
TATGTTTGGTAAGGGCCTACTGTATAAGAAG	1	241	1
CACCTAAGAAGCAAAACTTCTTATACAGTAG	1	257	0
AAACAAACAAAAGAAACATCAAGTTATTAAG	2	57	1
GTTTCGTGTGGAAGAGCATCTTAGCATAGGA	2	157	0
AACCATCAAAACAAAACTTCAAATATAAAAA	3	32	1
TCTGAGTTCTAAGAACCCTCTACCAGAGTCG	3	163	1
GCACGCACAAGCGAGTCATCTCTTCCATAGA	4	101	0
TAGCAGTTTGAACAAGCATCTCAAGGAATAG	5	83	0
TTCCTCTTTAAAAAACCTTCTTCCTAGGATT	5	158	1
CAGAGTTCTTAACGATCTTCTCAGCTGACAG	5	239	0
CTTTGTGTGTAAAAGGCTTCTATAGGAAGAG	6	42	0
TTTTGAGAAAGAGAAACTTCTTTATAGTTCT	6	78	0
CTTTCAGGATACCGAACTCCTAAAAAAAGCT	6	118	1
GAACTCCTAAAAAAAGCTTCTTTATTTAAAA	6	131	1
ATAACATACTACAAAGCACCTAATCGACATC	8	88	1
GCACAGAGAAAAAAAACTTCTTACTCTAGCA	8	131	1
          ***** *****
MAP Score: 17.7115

Motif 2
TTCTCATAGGCTCTCTTCGTTCCTATATTCG	1	62	1
TATGCTAAGATGCTCTTCCACACGAAACAAT	2	160	1
AACAATATAAAGCACTTCCTTCCCT      	2	185	1
CAGAGTCGCCACCTCTTCCTACTAGCGATAT	3	186	1
GAAAATCAGCCTCATTTCGTTTCTATGGAAG	4	80	1
CAAGCGAGTCATCTCTTCCATAGAAACGAAA	4	94	0
TCCTTTTTGCCTCTCTTTCTCCTGTGCCATA	4	132	0
     AAGGAAACACTTCCATAGTGCTGGAA	5	5	1
TTTCTGGAAGCACTCTTCCTTCTTCTATTCC	5	59	1
CTCTTCCTTCTTCTATTCCTTGAGATGCTTG	5	71	1
CTTTAAAAAACCTTCTTCCTAGGATTTTATA	5	163	1
TGACTAAAGGCACAATTCCACTCTAAAAAAG	5	268	1
GCGGCTGATTTGCTCTTCCTATAGAAGCCTT	6	30	1
ATAAAGAAGTTTCTCTTTCTCAAAAACACAA	6	84	1
AACAATCCGCCTTTCTTCGATTAGCCCTTCT	6	173	1
CAAAAGTATAATCATTTCCTTTTCAGCACTT	6	221	1
       TACCCCATTTCGTTTTTAGGACAA	7	3	1
          * *********
MAP Score: 13.8848

Motif 3
GGATAATGTATTTGATTATTTTTCACGAATGAA	1	106	0
TCCCTAGTCATATGAATATGTTTGGTAAGGGCC	1	225	1
GGGCCTACTGTATAAGAAGTTTTGCTTCTTAGG	1	253	1
TTAAAATTAATTTAAGCGTTTTTGCAAATTTTG	2	23	0
AAACTTCAAATATAAAAATTTTTATTTTGCTGA	3	45	1
TGCTGATGCTTAAAATAGATTTTTAGAAGAACT	3	72	1
CTTCCAGCACTATGGAAGTGTTTCCTT      	5	4	0
GCAAATGGTGTATAGTCAAATTTCTGTCAGCTG	5	216	1
TTGCTCTTCCTATAGAAGCCTTTTACACACAAA	6	39	1
CATAAAGAACTATAAAGAAGTTTCTCTTTCTCA	6	73	1
AATTTTTAAATAAAGAAGCTTTTTTTAGGAGTT	6	132	0
GGATTGTTCATATAAAAATTTTTAAATAAAGAA	6	148	0
TTTATCGGGTTATAGCTAATTTT          	8	0	0
TATAACCCGATAAAAAAGGTTTTCTTGAATTAA	8	19	1
TGTAGTATGTTATGAGGGGTTTTTGATTTAGAA	8	68	0
          *****  * ****
MAP Score: 11.6325

Motif 4
CTCATAGGCTCTCTTCGTTCCTATATTCGACA	1	64	1
ACACCTCCCGCGTTTCATTCGTGAAAAATAAT	1	93	1
CAATATAAAGCACTTCCTTCCCT         	2	187	1
GATCCATATCCCCCTCATTTCTAAGAAACCAT	3	221	0
AAATCAGCCTCATTTCGTTTCTATGGAAGAGA	4	82	1
CTCCTTTTTGCCTCTCTTTCTCCTGTGCCATA	4	132	0
TCTGGAAGCACTCTTCCTTCTTCTATTCCTTG	5	61	1
       GCTTATCTCCTGCTCTGCAAGCGGC	6	3	1
TATAAAGAAGTTTCTCTTTCTCAAAAACACAA	6	83	1
CTTCGATTAGCCCTTCTTGCTTAGAAAGATCA	6	187	1
AAAGTATAATCATTTCCTTTTCAGCACTTTAT	6	223	1
     TACCCCATTTCGTTTTTAGGACAACTC	7	5	1
          * **** *****
MAP Score: 9.82996

Motif 5
GTTAGGATGGTCGGGTTCTGTGTACTAGATCCCT	1	196	1
TATAAGAAGTTTTGCTTCTTAGGTGGGACGTCAT	1	263	1
GTTTCTTTTGTTTGTTTCTTAAAATTAATTTAAG	2	40	0
TTTGTTCTTATTGGATTTTAACTAGTTCAGATTC	2	95	0
GATGCTTAAAATAGATTTTTAGAAGAACTGGTTT	3	76	1
CGATATGGGGATGGTTTCTTAGAAATGAGGGGGA	3	211	1
TCAGCCTCATTTCGTTTCTATGGAAGAGATGACT	4	85	1
TACCTTAGACTTCGATTTTCTGGAAGCACTCTTC	5	43	1
TGAAAGGGTTTGTGTTTTTGAGAAAGAGAAACTT	6	90	0
AGTATAATCATTTCCTTTTCAGCACTTTATTTAG	6	225	1
   TACCCCATTTCGTTTTTAGGACAACTCC   	7	7	1
TAAGAATTAGTTTGATTTTTTCTAAATCAAAAAC	8	49	1
AAGATGTCGATTAGGTGCTTTGTAGTATGTTATG	8	87	0
          ** * **** ** *
MAP Score: 7.98049

Motif 6
TCAGCCGCTTGCAGAGCAGGAGATAAGC  	6	8	0
ATTTCTGTCAGCTGAGAAGATCGTTAAGAA	5	235	1
GTTTCTCTATTCAGAGGAGACTTGATAATA	3	106	1
GCTTCTATAGGAAGAGCAAATCAGCCGCTT	6	28	0
GCGTGCTATGGCACAGGAGAAAGAGAGGCA	4	126	1
TTCTTAGAACTCAGAGCAGGGATGGTACCC	3	148	0
TCGCTAGTAGGAAGAGGTGGCGACTCTGGT	3	184	0
CGTTTCTATGGAAGAGATGACTCGCTTGTG	4	97	1
TTTTCTCTGTGCAGAGAAATATAAGATGTC	8	113	0
GCATCTCAAGGAATAGAAGAAGGAAGAGTG	5	69	0
GAGCATCTTAGCATAGGAGTGTTTCTAGAT	2	145	0
ATTTCTCTGCACAGAGAAAAAAAACTTCTT	8	123	1
AAGGTTTTTTAAAGAGGAAATAGTGAATCC	5	147	0
TTCTGAAAATGCTGAGCTAAGTTATAGTTT	4	35	1
AGCCCTTCTTGCTTAGAAAGATCATCCAAA	6	195	1
GAAGAGAGCCTATGAGAAGGCTTGTAAATA	1	50	0
          **********
MAP Score: 5.84711

Motif 7
AGAAAGCTAGTAGCTCTGTGAATAATCTTGATTGT	1	148	1
GAAGAACTGGTTTCTCTATTCAGAGGAGACTTGAT	3	97	1
GATTCACTATTTCCTCTTTAAAAAACCTTCTTCCT	5	148	1
AAAGGCACAATTCCACTCTAAAAAAGGATACCCTT	5	273	1
AGCGGCTGATTTGCTCTTCCTATAGAAGCCTTTTA	6	29	1
TATAAAGAAGTTTCTCTTTCTCAAAAACACAAACC	6	83	1
ACATCTTATATTTCTCTGCACAGAGAAAAAAAACT	8	114	1
AAAAAACTTCTTACTCTAGCAAAAG          	8	141	1
          ** **** *  * **
MAP Score: 4.71114

Motif 8
TCCCACCTAAGAAGCAAAACTTCTTATACAGTAGGCCCTTACC	1	248	0
AATTTGCAAAAACGCTTAAATTAATTTTAAGAAACAAACAAAA	2	26	1
AAACAAACAAAAGAAACATCAAGTTATTAAGAAATAAAGAATC	2	57	1
AAGAACAAAAAAATCACAGAGATTGATCTAGAAACACTCCTAT	2	120	1
CGCAACCATCAAAACAAAACTTCAAATATAAAAATTTTTATTT	3	29	1
CATTTCTAAGAAACCATCCCCATATCGCTAGTAGGAAGAGGTG	3	195	0
GAGAACAGCCAAATCTCCAGCCACTATAGAATATCAGACTGCG	3	266	1
     AAGGAAACACTTCCATAGTGCTGGAAGATACTATACCT	5	5	1
TGCTTCCAGAAAATCGAAGTCTAAGGTATAGTATCTTCCAGCA	5	28	0
GCAGTTTGAACAAGCATCTCAAGGAATAGAAGAAGGAAGAGTG	5	69	0
TTTTACACACAAAGCATAAAGAACTATAAAGAAGTTTCTCTTT	6	59	1
TTCTCTTTCTCAAAAACACAAACCCTTTCAGGATACCGAACTC	6	94	1
CGAACTCCTAAAAAAAGCTTCTTTATTTAAAAATTTTTATATG	6	130	1
TGATCTTTCTAAGCAAGAAGGGCTAATCGAAGAAAGGCGGATT	6	176	0
TAGAAAAAATCAAACTAATTCTTAATTCAAGAAAACCTTTTTT	8	30	0
CTGCACAGAGAAAAAAAACTTCTTACTCTAGCAAAAG      	8	129	1
          *** ** *        *  ** *
MAP Score: 3.34922