AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons019_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252372
 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	TM1374	47	phosphoglycerate mutase
#9	TM1375	166	spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein
#10	TM1379	27	seryl-tRNA synthetase
#11	TM1400	204	aspartate aminotransferase, putative
#12	TM1627	30	general stress protein Ctc
#13	TM1631	62	conserved hypothetical protein

Motif 1
AATCTAAAATGGGAGGTGGTAAC       	7	194	1
AATTTCAACAGGGAGGGGATAGGC      	11	4	0
ATGCTTTTTCGGGAGGTGATTTCTAAGTGG	7	58	0
TTGGAAGACCCGGAGGTGATACT       	4	3	0
ATTGGAAGAAGGGAGGTATTG         	9	155	1
AAGCGGTCCGAGGAGGTGTGAAA       	7	3	0
ATTTTATCACGGGAGGTGGAGAGA      	6	4	0
TGTCTCCTTCCGGAGGGATTCAATATGTAT	13	36	0
CAAAAAGACCGGGAGGGAAGATC       	5	3	0
TTCTTTTTAATGGAGGGGTGTGAAGCATTT	5	176	1
TTCTCAAAAAAGGAGGGATTCAC       	1	74	1
AGACTTTGATTGGAGGTGATCGGG      	8	4	0
ATCTCAAATGTGGAGGTGATACTT      	6	121	1
TTGTGATAAGGGGAGGGATAAG        	10	15	1
GAAGACCTACGGGAGGGAGAAAAG      	12	16	1
CTATAATCTTGAGAGGTGTTGGGAATATTA	11	62	0
AAGCGGTCAAAGGCGGGGGTCTGCAAAATC	9	59	1
TCTCTGGAGGCGGCGGTGGGATTCGAACCC	9	98	0
AAACCTTATGAGGAGGTCTTATTGTGAAAA	2	32	1
TATACAACCCAGGAGGTCTTGAAAATTCCT	5	38	1
TTTTCTCGAAAGGAGGGAAAAAA       	4	202	1
TCAAATGTTTCAGAGGTGTGTAAGAAATAT	6	83	1
AAATAGAAACCAGAGGGAGGCCAGCGTAGC	5	80	1
GAAATGGAGCCAGCGGTGGGACTCGAACCC	5	149	0
          **********
MAP Score: 45.605

Motif 2
        AGTATCACCTCCGGGTCTTCCAAT	4	2	1
ATCATGGATATTTCACCGGTTGTAGATCCGTA	4	139	0
     TTTTTTCCCTCCTTTCGAGAAAAGTGT	4	198	0
     GATCTTCCCTCCCGGTCTTTTTGGATA	5	5	1
GTTTCTATTTTACCAGCCGCACAGGAATTTTC	5	58	0
TGGGTTCGAGTCCCACCGCTGGCTCCATTTCT	5	148	1
CGGAAATGCTTCACACCCCTCCATTAAAAAGA	5	177	0
          TCTCTCCACCTCCCGTGATAAA	6	0	1
       AAGTATCACCTCCACATTTGAGATG	6	120	0
        TTTCACACCTCCTCGGACCGCTTT	7	2	1
        GTTACCACCTCCCATTTTAGATTA	7	193	0
TGGGTTCGAATCCCACCGCCGCCTCCAGAGAG	9	97	1
      CTTATCCCTCCCCTTATCACAATTCT	10	11	0
TGTATAATATTCCCAACACCTCTCAAGATTAT	11	58	1
    CTTTTCTCCCTCCCGTAGGTCTTCGCAT	12	12	0
ACATATTGAATCCCTCCGGAAGGAGACACAAC	13	38	1
          ******* ** *
MAP Score: 19.2739

Motif 3
GTGAATTCTGCATCAAAGGGGGTATAATCAC	0	269	1
GGGTATAATCACGAGAAGAGGA         	0	288	1
TTTAATTCTCAAAAAAGGAGGGATTCAC   	1	69	1
AAAGTGGTTTAATAGAAGTGGCAAACCTTAT	2	10	1
AATTGGAAGACCCGGAGGTGATACT      	4	4	0
ATGTTATGTCCATAAGGGTGATATAATGAAA	4	33	0
GACACTTTTCTCGAAAGGAGGGAAAAAA   	4	197	1
AAAATAGAAACCAGAGGGAGGCCAGCGTAGC	5	79	1
ATTTCTTTTTAATGGAGGGGTGTGAAGCATT	5	174	1
AAATTTTATCACGGGAGGTGGAGAGA     	6	5	0
TAATACTAAATCTAAAAGAGGACATCAGAAA	6	34	0
CCATCTCAAATGTGGAGGTGATACTT     	6	119	1
AGATGCTTTTTCGGGAGGTGATTTCTAAGTG	7	59	0
ATAATCTAAAATGGGAGGTGGTAAC      	7	192	1
TTAGACTTTGATTGGAGGTGATCGGG     	8	5	0
TCAAAGTCTAACACAAAGAGGTGCATAGAAG	8	25	1
AGCCTGGCTCTCTGGAGGCGGCGGTGGGATT	9	105	0
TTTATATTGGAAGAAGGGAGGTATTG     	9	150	1
TAGAATTGTGATAAGGGGAGGGATAAG    	10	10	1
CAAATTTCAACAGGGAGGGGATAGGC     	11	5	0
TATTTATCAAAAGGAACGAGAAAGCAAAAAA	11	100	0
CACCACCATCCTGGAAAGGGGGAGTTCC   	11	186	1
CGAAGACCTACGGGAGGGAGAAAAG      	12	15	1
TTGAATCCCTCCGGAAGGAGACACAACGA  	13	43	1
          ******** **
MAP Score: 8.41912

Motif 4
AATTCTGCATCAAAGGGGGTATAATCACGAG	0	272	1
TAATTCTCAAAAAAGGAGGGATTCAC     	1	71	1
CACTTTTCTCGAAAGGAGGGAAAAAA     	4	199	1
TCCAAAAAGACCGGGAGGGAAGATC      	5	4	0
TAAAATAGAAACCAGAGGGAGGCCAGCGTAG	5	78	1
ATTTCTTTTTAATGGAGGGGTGTGAAGCATT	5	174	1
AAATTTTATCACGGGAGGTGGAGAGA     	6	5	0
TATAATCTAAAATGGGAGGTGGTAAC     	7	191	1
CCAAGCGGTCAAAGGCGGGGGTCTGCAAAAT	9	57	1
GAATTGTGATAAGGGGAGGGATAAG      	10	12	1
CAAATTTCAACAGGGAGGGGATAGGC     	11	5	0
CACCATCCTGGAAAGGGGGAGTTCC      	11	189	1
GCGAAGACCTACGGGAGGGAGAAAAG     	12	14	1
          ** ********
MAP Score: 6.0358

Motif 5
TAATTCTCAAAAAAGGAGGGATTCAC    	1	71	1
AACCTCGGTGACAGGCAGAGAAACATAGAA	3	24	1
CACTTTTCTCGAAAGGAGGGAAAAAA    	4	199	1
ATCCAAAAAGACCGGGAGGGAAGATC    	5	6	0
AATAGAAACCAGAGGGAGGCCAGCGTAGCT	5	81	1
GCTTTTTGAAGGAAGAAAGG          	5	233	1
GCTTTTTTACGGAGGAAGACTGGTGCTTTC	7	29	1
CCAAGCGGTCAAAGGCGGGGGTCTGCAAAA	9	57	1
TTTTTATATTGGAAGAAGGGAGGTATTG  	9	148	1
ACAAATTTCAACAGGGAGGGGATAGGC   	11	7	0
CCACCATCCTGGAAAGGGGGAGTTCC    	11	188	1
AAGACCTACGGGAGGGAGAAAAG       	12	17	1
GAATCCCTCCGGAAGGAGACACAACGA   	13	45	1
          **********
MAP Score: 5.73857

Motif 6
AAACACGAGTAATACTCATTTTTTATGATTAT	0	21	1
TCTTTGAGTTACAACTGATTTTATTCCCGATG	0	102	1
TTATTGTGAAAAAACTTATTTTGATCAGTTTG	2	50	1
GACGAATTTGAAGAAAGATTTCTGAGCTTTTT	5	208	1
AGAGGTGTGTAAGAAATATTTTACACCATCTC	6	94	1
CCAGTACAGAAAGAAAAATTTTTCAACGAACA	7	126	1
TGATGGTGTAAACACAAATTTCAACAGGGAGG	11	18	0
AAGATTATAGCAAACAGATTTTTTGCTTTCTC	11	82	1
          ** *** *****
MAP Score: 2.50042