AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions010_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251276
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0335	26	dihydroorotase
#1	TM0337	278	conserved hypothetical protein
#2	TM0338	184	hypothetical protein
#3	TM0558	211	carbamoyl-phosphate synthetase, small subunit
#4	TM1095	300	adenylosuccinate lyase
#5	TM1632	62	conserved hypothetical protein
#6	TM1642	35	aspartate carbamoyltransferase, catalytic and regulatory chains

Motif 1
          ACTTTTCCCTCCGAATTCCTT	0	15	0
GATATCATCATCCTTCGCCTGTAAATGTAGC	1	44	0
TTCTAACATCTTCTTCACCTCCTTTCAGATA	1	71	0
TGTTTTCCTGTGTTTTTCCACCAAAAATCTC	1	126	0
GCCGTACCCCTGCGTCCCCATTTTTTAACCA	1	182	1
AGGGTGATACTGTGTTTCTTCCCACAACACG	1	250	1
        ATTTTGTCACCTCCTGCAAAATA	2	2	1
TGTAAGGATTTTCGTTGCCCCTTTTCCCGCC	2	81	1
        TTATCGTCACTCCTTTGATTGGT	3	2	1
GGACCTCCCGTCTTTTTCTTTACTTTGAATT	3	148	0
  GTTGCACCTCCTTCCCTTTCTCAGAGATT	3	192	0
GTGAGTCTGATCTTTCTCCTCGTCCTCGAGG	4	30	1
TCGATCGTAATCTGTCCCTTTCAAATATTCG	4	65	0
GGTGCTGTCCTTCTTTCCTCTGATCGCCACC	4	110	1
ATGTTCACGGTTTTTTTCTTTGCGAAACTGG	4	139	0
CTTCTTATCTTGTTTTTCCTGTTGTTGCGCT	4	244	1
         CTTTTTCCCTCCCAAACAGATC	4	288	0
      TCGTTGTGTCTCCTTCCGGAGGGAT	5	4	1
        TTTCTGTTCCTCCACAGTGTTGT	5	49	0
          ****** ****
MAP Score: 16.6726

Motif 2
AGGAAAGGAATTCGGAGGGAAAAGT     	0	11	1
GATGATGATATCTGAAAGGAGGTGAAGAAG	1	63	1
AAAAAATTTTTCTGTAAGGATTTTCGTTGC	2	69	1
CTTTGATTGGTTTGGAAGGTGATGTTTAAG	3	22	1
GATTATACCCGCTGAAAGGACCTCCCGTCT	3	166	0
GTATAATCTCTGAGAAAGGGAAGGAGGTGC	3	188	1
GGTTCGAATATTTGAAAGGGACAGATTACG	4	61	1
AGAAAAGCGATTTGAGAGGTATGTTCACGG	4	160	0
GCGATGGCGTTGTGGAAGGTAGCGAGCATT	4	201	1
GAGAGATCTGTTTGGGAGGGAAAAAG    	4	284	1
ATTGAATCCCTCCGGAAGGAGACACAACGA	5	10	0
TATTTTTTTGTCTGAAGGGGGTATCGTGA 	6	16	1
          **********
MAP Score: 15.5628

Motif 3
TTATTCTTCTTTCTGTTTTCCTGTGTTTTTCCAC	1	136	0
GGCACTTACTTTTTGTTATTCTTCTTTCTGTTTT	1	151	0
AAAAAGTAAGTGCCGTACCCCTGCGTCCCCATTT	1	171	1
CATAGGGTGATACTGTGTTTCTTCCCACAACACG	1	247	1
         ATTTTGTCACCTCCTGCAAAATATT	2	1	1
CTGTAAGGATTTTCGTTGCCCCTTTTCCCGCCGT	2	80	1
         TTATCGTCACTCCTTTGATTGGTTT	3	1	1
CAAATTAAAGTCCTGTGACTTTCCTTTAATTCAA	3	121	1
TGAAAGGACCTCCCGTCTTTTTCTTTACTTTGAA	3	150	0
TTGTTTCTGGTGCTGTCCTTCTTTCCTCTGATCG	4	102	1
ATCTTGTTTTTCCTGTTGTTGCGCTCGTGTTCAC	4	250	1
         TCGTTGTGTCTCCTTCCGGAGGGAT	5	1	1
GTACAATACATATTGAATCCCTCCGGAAGGAGAC	5	17	0
         TTTCTGTTCCTCCACAGTGTTGTAC	5	47	0
          * ****  **** *
MAP Score: 10.9848

Motif 4
TATGTATTTTAAAACAAAAAAAGCCTCGTTTC	1	219	0
CGGTGTATTAAAAATCAAATAAGGCAATACTA	2	140	0
CATCACCTTCCAAACCAATCAAAGGAGTGACG	3	14	0
CAGGGTTCTGAAAACTAATAAACAATGGCTTA	3	48	0
TCCTTTAATTCAAAGTAAAGAAAAAGACGGGA	3	142	1
TGGTGGCGATCAGAGGAAAGAAGGACAGCACC	4	110	0
ACCAGTTTCGCAAAGAAAAAAACCGTGAACAT	4	138	1
ATCGCAACGAGAAACCAGAAAAGCGATTTGAG	4	174	0
AACAACAGGAAAAACAAGATAAGAAGCCGTTG	4	238	0
ATACCCCCTTCAGACAAAAAAATATCGCAC  	6	8	0
          ***** *** **
MAP Score: 9.88476

Motif 5
        CAGGAAAGGAATTCGGAGGGAAA	0	2	1
GAAAGGAATTCGGAGGGAAAAGT        	0	13	1
TGATGATATCTGAAAGGAGGTGAAGAAGATG	1	65	1
CACGTGTTGTGGGAAGAAACACAGTATCACC	1	252	0
AATATTTTGCAGGAGGTGACAAAAT      	2	4	0
TTCACGGCGGGAAAAGGGGCAACGAAAATCC	2	86	0
TGATTGGTTTGGAAGGTGATGTTTAAGCCAT	3	25	1
TTGAATTAAAGGAAAGTCACAGGACTTTAAT	3	124	0
TTAATTCAAAGTAAAGAAAAAGACGGGAGGT	3	146	1
ATAATCTCTGAGAAAGGGAAGGAGGTGCAAC	3	190	1
TTCGAATATTTGAAAGGGACAGATTACGATC	4	63	1
GGCGATCAGAGGAAAGAAGGACAGCACCAGA	4	107	0
ATGGCGTTGTGGAAGGTAGCGAGCATTAAAT	4	204	1
AGATCTGTTTGGGAGGGAAAAAG        	4	287	1
GAATCCCTCCGGAAGGAGACACAACGA    	5	6	0
TTTTTTTGTCTGAAGGGGGTATCGTGA    	6	18	1
          ********* *
MAP Score: 7.99185

Motif 6
GCAGGGGTACGGCACTTACTTTTTGTTATTCT	1	163	0
GCCTCGAAACGAGGCTTTTTTTGTTTTAAAAT	1	214	1
TACATAGGGTGATACTGTGTTTCTTCCCACAA	1	245	1
GCCGTGAAACGAGATTTTCTTTACATATAATT	2	109	1
TTAAAGTCCTGTGACTTTCCTTTAATTCAAAG	3	125	1
AGGACCTCCCGTCTTTTTCTTTACTTTGAATT	3	148	0
ACATGAAACAGGGTCTTTTCTC          	4	0	0
TGTTTCATGTGAGTCTGATCTTTCTCCTCGTC	4	22	1
AGTTGTTTCTGGTGCTGTCCTTCTTTCCTCTG	4	100	1
TATGTTCACGGTTTTTTTCTTTGCGAAACTGG	4	139	0
ATATCCAACGGCTTCTTATCTTGTTTTTCCTG	4	233	1
          * * ********
MAP Score: 6.31147

Motif 7
ATCAGTTCTAACATCTTCTTCACCTCCTTTCAG	1	74	0
TCTGTTTTCCTGTGTTTTTCCACCAAAAATCTC	1	126	0
ACTTACTTTTTGTTATTCTTCTTTCTGTTTTCC	1	149	0
AGGGTGATACTGTGTTTCTTCCCACAACACGTG	1	250	1
GGATTTTCGTTGCCCCTTTTCCCGCCGTGAAAC	2	86	1
CGCCGTGAAACGAGATTTTCTTTACATATAATT	2	108	1
ATTTGAAATTTGAGGATTTTCATGCAATGAATG	3	80	0
ATTAAAGTCCTGTGACTTTCCTTTAATTCAAAG	3	124	1
AAAGGACCTCCCGTCTTTTTCTTTACTTTGAAT	3	149	0
 GTTGCACCTCCTTCCCTTTCTCAGAGATTATA	3	189	0
CACATGAAACAGGGTCTTTTCTC          	4	0	0
TTCATGTGAGTCTGATCTTTCTCCTCGTCCTCG	4	25	1
TTGTTTCTGGTGCTGTCCTTCTTTCCTCTGATC	4	102	1
GGTATGTTCACGGTTTTTTTCTTTGCGAAACTG	4	140	0
AAATCGCTTTTCTGGTTTCTCGTTGCGATGGCG	4	177	1
CGGCTTCTTATCTTGTTTTTCCTGTTGTTGCGC	4	241	1
TCCCTCCCAAACAGATCTCTCGTGAACACGAGC	4	272	0
        TTTCTGTTCCTCCACAGTGTTGTAC	5	47	0
         GTGCGATATTTTTTTGTCTGAAGG	6	1	1
          ** * ****** *
MAP Score: 3.92537