AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons019_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252358
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0033	300	hypothetical protein
#1	TM0034	87	iron-sulfur cluster-binding protein
#2	TM0035	88	hypothetical protein
#3	TM0041	59	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
#4	TM0197	215	conserved hypothetical protein
#5	TM0579	243	conserved hypothetical protein
#6	TM0883	135	conserved hypothetical protein
#7	TM1162	207	conserved hypothetical protein
#8	TM1375	166	spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein
#9	TM1379	27	seryl-tRNA synthetase
#10	TM1400	204	aspartate aminotransferase, putative
#11	TM1627	30	general stress protein Ctc
#12	TM1631	62	conserved hypothetical protein

Motif 1
TTCTCAAAAAAGGAGGGATTCAC       	1	74	1
AAACCTTATGAGGAGGTCTTATTGTGAAAA	2	32	1
TTGGAAGACCCGGAGGTGATACT       	4	3	0
TTTTCTCGAAAGGAGGGAAAAAA       	4	202	1
CAAAAAGACCGGGAGGGAAGATC       	5	3	0
TATACAACCCAGGAGGTCTTGAAAATTCCT	5	38	1
AAATAGAAACCAGAGGGAGGCCAGCGTAGC	5	80	1
GAAATGGAGCCAGCGGTGGGACTCGAACCC	5	149	0
TTCTTTTTAATGGAGGGGTGTGAAGCATTT	5	176	1
ATTTTATCACGGGAGGTGGAGAGA      	6	4	0
TCAAATGTTTCAGAGGTGTGTAAGAAATAT	6	83	1
ATCTCAAATGTGGAGGTGATACTT      	6	121	1
AAGCGGTCCGAGGAGGTGTGAAA       	7	3	0
ATGCTTTTTCGGGAGGTGATTTCTAAGTGG	7	58	0
AATCTAAAATGGGAGGTGGTAAC       	7	194	1
AAGCGGTCAAAGGCGGGGGTCTGCAAAATC	8	59	1
TCTCTGGAGGCGGCGGTGGGATTCGAACCC	8	98	0
ATTGGAAGAAGGGAGGTATTG         	8	155	1
TTGTGATAAGGGGAGGGATAAG        	9	15	1
AATTTCAACAGGGAGGGGATAGGC      	10	4	0
CTATAATCTTGAGAGGTGTTGGGAATATTA	10	62	0
GAAGACCTACGGGAGGGAGAAAAG      	11	16	1
TGTCTCCTTCCGGAGGGATTCAATATGTAT	12	36	0
          **********
MAP Score: 42.9042

Motif 2
AATTCTGCATCAAAGGGGGTATAATCACGAG	0	272	1
TAATTCTCAAAAAAGGAGGGATTCAC     	1	71	1
TTGGAAGACCCGGAGGTGATACT        	4	2	0
GTTATGTCCATAAGGGTGATATAATGAAATT	4	31	0
CACTTTTCTCGAAAGGAGGGAAAAAA     	4	199	1
ATTCGTAATGCGCAGGTTGTGGGTTCGAGTC	5	129	1
GAAATGGAGCCAGCGGTGGGACTCGAACCCA	5	148	0
TCTTTTTAATGGAGGGGTGTGAAGCATTTCC	5	177	1
TTATCACGGGAGGTGGAGAGA          	6	0	0
ATCTCAAATGTGGAGGTGATACTT       	6	121	1
AAAAAGCGGTCCGAGGAGGTGTGAAA     	7	5	0
ATGCTTTTTCGGGAGGTGATTTCTAAGTGGA	7	57	0
AATCTAAAATGGGAGGTGGTAAC        	7	194	1
TATTCTATGTGGATGGCGGCGTAGCCAAGCG	8	33	1
GCCAAGCGGTCAAAGGCGGGGGTCTGCAAAA	8	56	1
TCTCTGGAGGCGGCGGTGGGATTCGAACCCA	8	97	0
TATATTGGAAGAAGGGAGGTATTG       	8	152	1
GAATTGTGATAAGGGGAGGGATAAG      	9	12	1
AATTTCAACAGGGAGGGGATAGGC       	10	3	0
CCCCTTTCCAGGATGGTGGTGCTTGTTATTT	10	176	0
AAGACCTACGGGAGGGAGAAAAG        	11	17	1
GAATCCCTCCGGAAGGAGACACAACGA    	12	45	1
          ****** ****
MAP Score: 14.2232

Motif 3
AGAAACATAGAAAAAGCCCTTGAGGAA       	3	42	1
GATCCGTACGAAAAATCGAATTCGGTGAATCTAA	4	113	0
TATAATATCCAAAAAGACCGGGAGGGAAGATC  	5	8	0
GGAGGTCTTGAAAATTCCTGTGCGGCTGGTAAAA	5	49	1
CCCCTCCATTAAAAAGAAATGGAGCCAGCGGTGG	5	160	0
CTTCCTCCGTAAAAAAGCGGTCCGAGGAGGTGTG	7	13	0
TCACCTCCCGAAAAAGCATCTGCGTAGAACTATT	7	69	1
GGGGGTCTGCAAAATCCCTATTCGTGGGTTCGAA	8	73	1
CTTCCAATATAAAAAGCCAGGCCGTGTAGCCTGG	8	129	0
ACGAGAAAGCAAAAAATCTGTTTGCTATAATCTT	10	82	0
ATCCGTCTGTAAAAATTCTGGTAGTATAATTAGT	10	137	1
          *****  *  ****
MAP Score: 7.1589

Motif 4
AATTCTCAAAAAAGGAGGGATTCAC     	1	72	1
ATTGGAAGACCCGGAGGTGATACT      	4	4	0
ACTTTTCTCGAAAGGAGGGAAAAAA     	4	200	1
TCCAAAAAGACCGGGAGGGAAGATC     	5	5	0
TAAAATAGAAACCAGAGGGAGGCCAGCGTA	5	78	1
AAATGGAGCCAGCGGTGGGACTCGAACCCA	5	148	0
ATTTCTTTTTAATGGAGGGGTGTGAAGCAT	5	174	1
TATCACGGGAGGTGGAGAGA          	6	0	0
AGCGGTCCGAGGAGGTGTGAAA        	7	2	0
GATGCTTTTTCGGGAGGTGATTTCTAAGTG	7	59	0
CCAAGCGGTCAAAGGCGGGGGTCTGCAAAA	8	57	1
TTCGAACCCACGAATAGGGATTTTGCAGAC	8	77	0
CTCTGGAGGCGGCGGTGGGATTCGAACCCA	8	97	0
TTTTATATTGGAAGAAGGGAGGTATTG   	8	149	1
         TAGAATTGTGATAAGGGGAGG	9	1	1
AATTGTGATAAGGGGAGGGATAAG      	9	13	1
AAATTTCAACAGGGAGGGGATAGGC     	10	5	0
CACCATCCTGGAAAGGGGGAGTTCC     	10	189	1
GCGAAGACCTACGGGAGGGAGAAAAG    	11	14	1
TGTGTCTCCTTCCGGAGGGATTCAATATGT	12	38	0
          **********
MAP Score: 6.43179

Motif 5
AATGTGTGTAACAAAAAATCCATCGAAATC	0	173	1
TAGAATTTAAGTGAAAAATCATACACCTCA	1	16	1
AGGTCTTATTGTGAAAAAACTTATTTTGAT	2	45	1
GTAGATCCGTACGAAAAATCGAATTCGGTG	4	120	0
TCTACAACCGGTGAAATATCCATGATACAA	4	145	1
GTCTTCCTCCGTAAAAAAGCGGTCCGAGGA	7	19	0
AAATCACCTCCCGAAAAAGCATCTGCGTAG	7	66	1
AGGCGGGGGTCTGCAAAATCCCTATTCGTG	8	69	1
GAACGAGAAAGCAAAAAATCTGTTTGCTAT	10	88	0
TCATCCGTCTGTAAAAATTCTGGTAGTATA	10	135	1
          **********
MAP Score: 5.88527