AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251264
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0335	26	dihydroorotase
#1	TM0337	278	conserved hypothetical protein
#2	TM0558	211	carbamoyl-phosphate synthetase, small subunit
#3	TM1095	300	adenylosuccinate lyase
#4	TM1632	62	conserved hypothetical protein
#5	TM1642	35	aspartate carbamoyltransferase, catalytic and regulatory chains

Motif 1
AGGAAAGGAATTCGGAGGGAAAAGT      	0	11	1
GATGATGATATCTGAAAGGAGGTGAAGAAGA	1	63	1
CCTCACGTGTTGTGGGAAGAAACACAGTATC	1	255	0
CTTTGATTGGTTTGGAAGGTGATGTTTAAGC	2	22	1
GTATAATCTCTGAGAAAGGGAAGGAGGTGCA	2	188	1
GGTTCGAATATTTGAAAGGGACAGATTACGA	3	61	1
AGAAAAGCGATTTGAGAGGTATGTTCACGGT	3	159	0
GCGATGGCGTTGTGGAAGGTAGCGAGCATTA	3	201	1
GAGAGATCTGTTTGGGAGGGAAAAAG     	3	284	1
ATTGAATCCCTCCGGAAGGAGACACAACGA 	4	9	0
TATTTTTTTGTCTGAAGGGGGTATCGTGA  	5	16	1
          ********* *
MAP Score: 17.2174

Motif 2
CCCTCCGAATTCCTTTCCTG          	0	0	0
          ACTTTTCCCTCCGAATTCCT	0	16	0
GATATCATCATCCTTCGCCTGTAAATGTAG	1	45	0
TGTTTTCCTGTGTTTTTCCACCAAAAATCT	1	127	0
TTCTTCTTTCTGTTTTCCTGTGTTTTTCCA	1	137	0
GCCGTACCCCTGCGTCCCCATTTTTTAACC	1	182	1
AGGGTGATACTGTGTTTCTTCCCACAACAC	1	250	1
GGACCTCCCGTCTTTTTCTTTACTTTGAAT	2	149	0
  GTTGCACCTCCTTCCCTTTCTCAGAGAT	2	193	0
GTGAGTCTGATCTTTCTCCTCGTCCTCGAG	3	30	1
TCGATCGTAATCTGTCCCTTTCAAATATTC	3	66	0
GGTGCTGTCCTTCTTTCCTCTGATCGCCAC	3	110	1
ATGTTCACGGTTTTTTTCTTTGCGAAACTG	3	140	0
CTTCTTATCTTGTTTTTCCTGTTGTTGCGC	3	244	1
         CTTTTTCCCTCCCAAACAGAT	3	289	0
      TCGTTGTGTCTCCTTCCGGAGGGA	4	4	1
        TTTCTGTTCCTCCACAGTGTTG	4	50	0
          **********
MAP Score: 16.5036

Motif 3
ATGATGATATCTGAAAGGAGGTGAAGAAGA	1	64	1
TGAATCCCTCCGGAAGGAGACACAACGA  	4	8	0
         CAGGAAAGGAATTCGGAGGGA	0	1	1
ATTTTTTTGTCTGAAGGGGGTATCGTGA  	5	17	1
TGGCGATCAGAGGAAAGAAGGACAGCACCA	3	109	0
CCACCAGTTTCGCAAAGAAAAAAACCGTGA	3	136	1
GAGATCTGTTTGGGAGGGAAAAAG      	3	286	1
GATGGCGTTGTGGAAGGTAGCGAGCATTAA	3	203	1
GTTCGAATATTTGAAAGGGACAGATTACGA	3	62	1
TCACGTGTTGTGGGAAGAAACACAGTATCA	1	254	0
TCTCTGAGAAAGGGAAGGAGGTGCAAC   	2	194	1
TTGATTGGTTTGGAAGGTGATGTTTAAGCC	2	24	1
ATTATACCCGCTGAAAGGACCTCCCGTCTT	2	165	0
GAAAGGAATTCGGAGGGAAAAGT       	0	13	1
CACAGGAAAACAGAAAGAAGAATAACAAAA	1	145	1
TTCCAAACCAATCAAAGGAGTGACGATAA 	2	9	0
ACAACGCCATCGCAACGAGAAACCAGAAAA	3	184	0
TTTCCTTTAATTCAAAGTAAAGAAAAAGAC	2	140	1
          **********
MAP Score: 13.9161

Motif 4
GAAAGGAATTCGGAGGGAAAAGT        	0	13	1
ACATTTACAGGCGAAGGATGATGATATCTGA	1	47	1
GAGATTTTTGGTGGAAAAACACAGGAAAACA	1	126	1
CACAGGAAAACAGAAAGAAGAATAACAAAAA	1	145	1
CACGTGTTGTGGGAAGAAACACAGTATCACC	1	252	0
TTAATTCAAAGTAAAGAAAAAGACGGGAGGT	2	146	1
CGAGGACGAGGAGAAAGATCAGACTCACATG	3	27	0
TGGTGGCGATCAGAGGAAAGAAGGACAGCAC	3	111	0
CACCAGTTTCGCAAAGAAAAAAACCGTGAAC	3	137	1
AGCGCAACAACAGGAAAAACAAGATAAGAAG	3	244	0
AGATCTGTTTGGGAGGGAAAAAG        	3	287	1
TTGAATCCCTCCGGAAGGAGACACAACGA  	4	8	0
GTACAACACTGTGGAGGAACAGAAA      	4	47	1
          * *********
MAP Score: 10.0464

Motif 5
         CAGGAAAGGAATTCGGAGGGA	0	1	1
AGGAAAGGAATTCGGAGGGAAAAGT     	0	11	1
CGATGCTACATTTACAGGCGAAGGATGATG	1	40	1
GATGATGATATCTGAAAGGAGGTGAAGAAG	1	63	1
CATAGAGATTTTTGGTGGAAAAACACAGGA	1	122	1
GGTTAAAAAATGGGGACGCAGGGGTACGGC	1	182	0
TAACCAGGCCTCGAAACGAGGCTTTTTTTG	1	207	1
TCACGTGTTGTGGGAAGAAACACAGTATCA	1	254	0
TTCCCACAACACGTGAGGAA          	1	268	1
TTTGATTGGTTTGGAAGGTGATGTTTAAGC	2	23	1
TCTCTGAGAAAGGGAAGGAGGTGCAAC   	2	194	1
GTTCGAATATTTGAAAGGGACAGATTACGA	3	62	1
ACTGGTGGCGATCAGAGGAAAGAAGGACAG	3	114	0
GAAAAGCGATTTGAGAGGTATGTTCACGGT	3	159	0
GGTTTCTCGTTGCGATGGCGTTGTGGAAGG	3	190	1
AGAGATCTGTTTGGGAGGGAAAAAG     	3	285	1
TGTGTCTCCTTCCGGAGGGATTCAATATGT	4	14	1
TGTACAACACTGTGGAGGAACAGAAA    	4	46	1
TATTTTTTTGTCTGAAGGGGGTATCGTGA 	5	16	1
          **********
MAP Score: 2.36545