AlignACE 3.0 10/20/99
AlignACE2 -i AA/AA_fusions007_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234479
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	pyrD	125	dihydroorotase dehydrogenase
#1	dmsB2	232	dimethylsulfoxide reductase chain B
#2	fdoG	212	formate dehydrogenase alpha subunit
#3	cysM	41	cysteine synthase, O-acetylserine (thiol) lyase B
#4	aq_1558	27	putative protein
#5	gltB	30	glutamate synthase large subunit
#6	gltD	39	glutamate synthase small subunit gltD

Motif 1
CCACCTCCTGAAATTTAAGTAAACCAAACTATA	0	14	1
TCGGCGGTGAAAATTTTTATAAAAATTTCGTTA	0	56	1
AAATTTCGTTATATATACATAAAGTTAATTAAA	0	78	1
GCCGATAAGGAAAGTCGTAAAACCGATTAACGG	1	149	1
ATTCAATGAAAATGTTCGAAAAA          	2	0	0
TTTTCATTGAATAATTAAATAAATAAGTTATGT	2	21	1
CTTATATTCAAATATCACATAACTTATTTATTT	2	37	0
TTTCAAAACAATATTTTAAAAATAGGCATATGA	2	116	0
AAAAAAGACAAAATTTTCAAAACAATATTTTAA	2	130	0
AATCATGAAAAAATTTAAAAAAAAGACAAAATT	2	148	0
TGAAAGGGGAATAAACTAAAAACTAAGAATGCT	2	181	1
  AATGTAGGATATTCTAATAAAAACTTA    	4	6	0
          ATACTCTCAAAACTCTTAAGGGG	5	0	1
          *** **  *****
MAP Score: 12.3657

Motif 2
AAAGTTAATTAAAGGTTAGGAAGTTAAAATA	0	98	1
TGAAAGTAAGAAGGATGAGGAGCTGAATGAA	1	33	0
TTCCCGAGGTAAGGAGAAGTAAAATTTACTG	1	85	1
TCGGCTCTAAAAAGGGAGACACTATCCAGTC	1	123	0
GATAAGTATTAAGGGGGAAAAGTCAATGCCG	1	179	0
TAGAGAGTATAAGGATAAGTATTAAGGGGGA	1	192	0
TCATGATTTGAAAGGGGAATAAACTAAAAAC	2	173	1
CAAAACTCTTAAGGGGTGGCAGA        	5	17	1
          ********* *
MAP Score: 7.40274

Motif 3
    AATACCACCTCCTGAAATTTAAGTAAACCA	0	6	1
GTTTATTTTAACTTCCTAACCTTTAATTAACTTT	0	98	0
GTCTTCATTCAGCTCCTCATCCTTCTTACTTTCA	1	30	1
CATTGACTTTTCCCCCTTAATACTTATCCTTATA	1	182	1
ATACTCTCTATCCTCCTGAGGATACTCAG     	1	213	1
    TCTGCCACCCCTTAAGAGTTTTGAGAGTAT	5	10	0
GATGATAAACTCTCCTTTAAGATATTCAAGTT  	6	8	0
          ******* *   **
MAP Score: 1.65738

Motif 4
AACGAAATTTTTATAAAAATTTTCACCGCCGAGTAG	0	52	0
TTATGTATATATAACGAAATTTTTATAAAAATTTTC	0	64	0
        TTTTTCGAACATTTTCATTGAATAATTA	2	2	1
AAATAGGCATATGAACATTTTTTTATTGTGTATCAA	2	94	0
TATGCCTATTTTTAAAATATTGTTTTGAAAATTTTG	2	119	1
AAATATTGTTTTGAAAATTTTGTCTTTTTTTTAAAT	2	133	1
TTTGTCTTTTTTTTAAATTTTTTCATGATTTGAAAG	2	151	1
CTCCGAGACCTTTAAAATAGTATCATACCGCCCT  	3	17	1
        AATGTAGGATATTCTAATAAAAACTTA 	4	9	0
GAATATCTTAAAGGAGAGTTTATCATCTTAACCT  	6	15	1
          **    * *** ****
MAP Score: 1.10954