AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_fusions012_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234571
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	nirB	120	nitrite reductase (NAD(P)H) large subunit
#1	aq_1236	23	hypothetical protein
#2	cysG	161	siroheme synthase
#3	hemA	38	glutamyl tRNA reductase (delta-aminolevulinate synthase)
#4	aq_1771	300	putative protein

Motif 1
CTCCTCCTGAGGAAACTCTTGCAAAAAACGT	0	93	0
AAGTGGCTCTGGAAAACGCGGAGGAGTTCAC	2	15	1
AGGAGTTCACGGGAAAGGTTTACAAGCTTTA	2	36	1
CTCTTCGTGAGGTAAAGCTTGTAAACCTTTC	2	48	0
AGGGTGAGAAGGGAAAGGCGATTGTGGACGC	2	108	1
ACGCACTCACGGGAAAAGTTGTAAAATTCTT	2	135	1
AGTTGAAAGTGGAAAATGCTGCAAAAACAAA	4	250	1
AAAACAAAAAGGAAAAAGCTGAGGTTCCTAA	4	273	1
          ****** ****
MAP Score: 13.5512

Motif 2
TAACTTTCATTTTACAACCTCTGTAAGGACTTAC	0	31	1
TGGCACGTTTTTTGCAAGAGTTTCCTCAGGAGGA	0	89	1
ACGGGAAAGGTTTACAAGCTTTACCTCACGAAGA	2	44	1
CTTGAAGAATTTTACAACTTTTCCCGTGAGTGCG	2	136	0
CCATCCTTGATTTTCAATCTTTTTAGCT      	4	4	0
TGAGTATACCTTTATAAAATTTCCATCCTTGATT	4	26	0
CCTTTTTGTTTTTGCAGCATTTTCCACTTTCAAC	4	251	0
          *** ***  *** *
MAP Score: 9.72888

Motif 3
GGCACGTTTTTTGCAAGAGTTTCCTCAGGAGGAGTGAAAG    	0	90	1
TTGTAAACCTTTCCCGTGAACTCCTCCGCGTTTTCCAGAGCCAC	2	17	0
CGGGAAAGGTTTACAAGCTTTACCTCACGAAGAGGCGCTCTGGA	2	45	1
TTTACAACTTTTCCCGTGAGTGCGTCCACAATCGCCTTTCCCTT	2	116	0
TAGCGGAAATTAACATTCGTTTCGTGAAGGTTAGGTGTCTAATA	4	79	1
GCACACAGGGTTTCTAATGTACCGTGTGGAGTTGAAAGTTGAAA	4	156	1
AAAGTTGAAAGAGCTAAAGCAACCGCACCGATGGTTATGAGTTT	4	190	1
TGGTTATGAGTTTCTAATGTACCGTGTGGAGTTGAAAGTGGAAA	4	221	1
         GGTACATTAGGAACCTCAGCTTTTTCCTTTTTGTT	4	275	0
          ** *        ****  *  * *
MAP Score: 7.65744

Motif 4
        CGCTAAAGTGGCTCTGGAAAAC	2	2	1
CACAGGGTTTCTAATGTACCGTGTGGAGTT	4	159	1
GTTGAAAGAGCTAAAGCAACCGCACCGATG	4	193	1
TTATGAGTTTCTAATGTACCGTGTGGAGTT	4	224	1
GCTGAGGTTCCTAATGTACC          	4	290	1
          **********
MAP Score: 7.61226

Motif 5
TATAACTTTCATTTTACAACCTCTGTAAGGACT	0	29	1
TGAGGTAAAGCTTGTAAACCTTTCCCGTGAACT	2	39	0
ATCGCCTTTCCCTTCTCACCCTTAATCTTATAA	2	97	0
 TCTTGAAGAATTTTACAACTTTTCCCGTGAGT	2	139	0
TCCATCCTTGATTTTCAATCTTTTTAGCT    	4	6	0
ACCTTTATAAAATTTCCATCCTTGATTTTCAAT	4	20	0
GTTGCTTTAGCTCTTTCAACTTTCAACTCCACA	4	180	0
TTTTTGCAGCATTTTCCACTTTCAACTCCACAC	4	244	0
          * *** ** ****
MAP Score: 3.68637

Motif 6
TTACAGAGGTTGTAAAATGAAAGTTATACG	0	27	0
CATAACTACCCGGAACTTTTTGGCACGTTT	0	69	1
AAAGTGGCTCTGGAAAACGCGGAGGAGTTC	2	14	1
AGAGGCGCTCTGGAGATTGCCTTTATAAGA	2	75	1
CGGGAAAAGTTGTAAAATTCTTCAAGA   	2	144	1
AAATCAAGGATGGAAATTTTATAAAGGTAT	4	25	1
ACGAAACGAATGTTAATTTCCGCTAACCCG	4	74	0
GAGTTGAAAGTGGAAAATGCTGCAAAAACA	4	249	1
          **********
MAP Score: 2.20348

Motif 7
   CTTTCACTCCTCCTGAGGAAACTCTTG	0	103	0
CTCCTCCGCGTTTTCCAGAGCCACTTTAGC	2	11	0
CTTTCCCGTGAACTCCTCCGCGTTTTCCAG	2	23	0
GTTTACAAGCTTTACCTCACGAAGAGGCGC	2	53	1
TATAAAGGCAATCTCCAGAGCGCCTCTTCG	2	72	0
CCTTTATAAAATTTCCATCCTTGATTTTCA	4	22	0
TTCAACTTTCAACTCCACACGGTACATTAG	4	169	0
TTCCACTTTCAACTCCACACGGTACATTAG	4	234	0
          **********
MAP Score: 1.18885