AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions017_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246686
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	narB	300	nitrate reductase
#1	hoxU	26	hydrogenase subunit
#2	hypothetical	40	hypothetical protein
#3	hoxF	76	hydrogenase subunit
#4	potential	300	potential NAD-reducing hydrogenase subunit

Motif 1
TGACAGTGATAATCAGCTTTGCTACTATCGCAATAGTG	0	52	1
TGCCATCAATAATTATCTGCTGTAATTTATTGCCACTA	0	85	0
CGCCAGGAAAAATCAGTTTTTCCTTATTCCAGGTGCCA	0	118	0
CCTCAGGACAAATTAACTATTAAAGTTTTTCACTGCGA	0	179	1
TATTAACTGTATTCATCTTTTGGTCAATTAGTGGTCAA	0	235	1
AATTCGCTTCAATTAACTGCCAATATTTTA        	0	280	1
AAGATCAAGCAATCACCTGATACTTAATATCCG     	3	5	0
TTGTTGCTTAAAACAACTTTTTCGTTGTCTAAATTATC	4	31	1
TTCATTGTTACATCAACTTTTAAAAAGTGAGCAAATCT	4	101	0
TCGCAATCAAATTTACCTGGTTTAGGCTCTCCCAATCA	4	232	1
AGGCTCTCCCAATCATCTTTTATCTGCTGTATTGCTCC	4	255	1
          ***** *** *      *
MAP Score: 12.1376

Motif 2
TTATCTGCTGTAATTTATTGCCACTATTGCG	0	80	0
CAGCAGATAATTATTGATGGCACCTGGAATA	0	101	1
GAAAAACTGATTTTTCCTGGCGAACAGTTAT	0	134	1
CGAACAGTTATTATTTTGGGCTAGCCCTCAG	0	154	1
GATTGGTCGATATTTGATCGCAGTGAAAAAC	0	203	0
ATTTTCAAAGGAGTTTTTGGCCA        	1	13	1
TATTTGAACTATTTTTGTTGCTTAAAACAAC	4	17	1
TTAAAACAACTTTTTCGTTGTCTAAATTATC	4	38	1
ATGGAATCTCTAGTTGGTTGCCTTCATTGTT	4	130	0
ATTCCATTCGTTATTGTGGGCAAGATTGTGG	4	154	1
GTCGGGAAAGAATTTGTGTGCCTCCACAATC	4	177	0
AAACCAGGTAAATTTGATTGCGAAAGTTAGC	4	224	0
          ****** ****
MAP Score: 7.26513

Motif 3
CAGCAGATAATTATTGATGGCACCTGGAATA	0	101	1
CAGTTTTTCCTTATTCCAGGTGCCATCAATA	0	112	0
GAAAAACTGATTTTTCCTGGCGAACAGTTAT	0	134	1
ACTATTAAAGTTTTTCACTGCGATCAAATAT	0	194	1
ATTTGAACTATTTTTGTTGCTTAAAACAACT	4	18	1
TTAAAACAACTTTTTCGTTGTCTAAATTATC	4	38	1
ATTCCATTCGTTATTGTGGGCAAGATTGTGG	4	154	1
GTATTGCTCCTTTTTGAGGATTTTTCC    	4	283	1
          ****** ****
MAP Score: 1.80984