AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions019_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251467
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0186	300	response regulator
#1	TM0402	300	ammonium transporter
#2	TM0404	47	deoxycytidylate deaminase, putative
#3	TM1358	50	conserved hypothetical protein
#4	TM1580	118	transcriptional regulator, putative

Motif 1
ATCTTACCACACGAAAGGGAGGAAAGAGGAACGG	4	11	0
     GGTTTCCTTTCGGGAGGAGAAACCTCCTC	2	5	1
GGGAGGCCGAAAAAAGGGGAGGAGGTTTCTCCTC	2	23	0
ATGATAAACTAAAAGTGGGAGGGATAAATT    	3	6	0
GTTTATCATTAAATAGTGGAGGATAGATT     	3	31	1
TTCGGGAATAAATTTCTGGAGGATTTTATATGTC	1	109	0
TGAAGTACACACCTTCTGGAAGAGTGGTTCTCAA	0	91	1
CAGGTTCAAAACCAGTGCGAGGAAAGCATCTTTG	0	44	0
TTTTATCCCTCCTGAGGGGAAGGGTTATTACGAA	0	276	0
AAACATATTTACCAAAAGGAGGTGTTTTT     	1	281	1
CGGGGCTGATACCGTGTTGAGGGTCCTCATCAGA	4	67	1
TGACGATTATACAACCCGGAGTGTTAACAATCTT	1	16	1
TGACACAGGACCGGGTTTGAAGGAACAAAACGGA	0	164	1
          **    ********
MAP Score: 11.243

Motif 2
AAGAGTGGTTCTCAAAATAGAAAAGAAAAATGATAA	0	110	1
TTGCGTGTTTCTGACACAGGACCGGGTTTGAAGGAA	0	153	1
GGTTTGAAGGAACAAAACGGATTTGGACTCTTCACA	0	177	1
CGATGGAAGTCATAAAAAAGGACGGGACCACATTCG	0	244	1
AATATCTAATCCAACATGGGGTTTGTGCCCTCTAAA	1	154	1
   GGGAGGCCGAAAAAAGGGGAGGAGGTTTCTCCT	2	24	0
TAATGATAAACTAAAAGTGGGAGGGATAAATT    	3	6	0
TTAGTTTATCATTAAATAGTGGAGGATAGATT    	3	28	1
CACGAAAGGGAGGAAAGAGGAACGGA          	4	0	0
ACGGAAGCAACGGACAACGGGGCTGATACCGTGTTG	4	50	1
          *  ***  ***  ***
MAP Score: 10.7144

Motif 3
TCTCAAAATAGAAAAGAAAAATGATAAAATC	0	119	1
GACCGGGTTTGAAGGAACAAAACGGATTTGG	0	172	1
TGGTTCGATGGAAGTCATAAAAAAGGACGGG	0	239	1
CTTCCCCTCAGGAGGGATAAAA         	0	288	1
CTTTTTTTTAGAGGGCACAAACCCCATGTTG	1	165	0
GTTTCCTTTCGGGAGGAGAAACCTCCTCCCC	2	11	1
         GGGAGGCCGAAAAAAGGGGAGG	2	35	0
ACTAAAAGTGGGAGGGATAAATT        	3	2	0
CCACACGAAAGGGAGGAAAGAGGAACGGA  	4	8	0
          ******* ***
MAP Score: 10.4953

Motif 4
AAAGATGCTTTCCTCGCACTGGTTTTGAAC	0	45	1
TCCTTCAAACCCGGTCCTGTGTCAGAAACA	0	158	0
CGAATGTGGTCCCGTCCTTTTTTATGACTT	0	250	0
TTCGTAATAACCCTTCCCCTCAGGAGGGAT	0	276	1
GTGTTAACAATCTTCCCAGTCAAACTGAAA	1	36	1
AGGAGAAACCTCCTCCCCTTTTTTCGGCCT	2	24	1
   AATTTATCCCTCCCACTTTTAGTTTAT	3	7	1
         TCCGTTCCTCTTTCCTCCCTT	4	1	1
CGTTCCTCTTTCCTCCCTTTCGTGTGGTAA	4	12	1
CAACACGGTATCAGCCCCGTTGTCCGTTGC	4	56	0
          **********
MAP Score: 9.76543

Motif 5
CGATTTCGAGTTCGTCGAATTCCATTTCGAT	0	12	0
GGAAAGCATCTTTGTCGATTTCGAGTTCGTC	0	27	0
CAAAGATGCTTTCCTCGCACTGGTTTTGAAC	0	44	1
CCAAATCCGTTTTGTTCCTTCAAACCCGGTC	0	172	0
TTTTATGACTTCCATCGAACCATTCAGATAG	0	230	0
CGAATGTGGTCCCGTCCTTTTTTATGACTTC	0	249	0
TTCGTAATAACCCTTCCCCTCAGGAGGGATA	0	276	1
         TTTTATCCCTCCTGAGGGGAAG	0	288	0
     AAAAACACCTCCTTTTGGTAAATATG	1	284	0
GGGGAGGAGGTTTCTCCTCCCGAAAGGAAAC	2	11	0
GAGGAGAAACCTCCTCCCCTTTTTTCGGCCT	2	23	1
        AATTTATCCCTCCCACTTTTAGT	3	2	1
          TCCGTTCCTCTTTCCTCCCTT	4	0	1
CCGTTCCTCTTTCCTCCCTTTCGTGTGGTAA	4	11	1
AGCCCCGTTGTCCGTTGCTTCCGTTTCAAAT	4	43	0
          *** *******
MAP Score: 4.58295