AlignACE 3.0 10/20/99
AlignACE2 -i BB/BB_operons019_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237624
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	BB0008	96	conserved hypothetical protein
#1	BB0053	81	uracil DNA glycosylase (ung)
#2	BB0115	139	ribosomal protein S6 (rpsF)
#3	BB0116	173	PTS system, maltose and glucose-specific IIABC component (malX)
#4	BBG29	300	conserved hypothetical protein
#5	BBG31	176	conserved hypothetical protein
#6	BBG32	27	replicative DNA helicase, putative

Motif 1
AAAAATTAAATTTCAAAAATAACAAATCAGTCCTT	1	13	1
AATAATTTCCTTTTTAAAAAAAGAATGATTCTGAA	5	124	0
TTTTTGGATTTTTTTAAGACAAAAAACACGAATTG	4	118	1
TTAAGACGCATTTCCTAAAAAATAAGCCTCTCCAT	4	170	0
TAGTTTGCAATTTGAAATATATTAAAGGACTGATT	1	37	0
GTATAACGTTTTTGCTAAAAATCAAAAAACCAAAA	4	81	1
AGACTAATTTTTTTCAACAATAAAAATTTTTATAA	2	44	0
AAATATTAGCTTTAGAATAGTAAAAAGACCAGTAA	5	38	1
TAAAGCTTTTTTTGCAAAAAAAAACTTTACTTACT	3	134	0
CAAAAAAAGCTTTATAATAAAATAGTGT       	3	155	1
TTCAGTTACATTTTGTATATTATAAAAATTTTTAT	2	25	1
TTGCAAACTATTTCTTATATAATACAAAA      	1	62	1
GTATTATATATTTTTTATAAATAAGTGATAAAACG	3	21	0
AATTGTAGCTTTTTCTCAAGATCAAATTAAATCTT	3	64	1
ATTAGTATAATATAAAATATATAAATAAGCACAGT	0	43	0
AAAAAAAAATTTTAAAGGAAAATAAAGTTTAAGTC	4	203	1
          ***  ** * ** **
MAP Score: 25.3246

Motif 2
TTTTTTGCAAAAAAAAACTTTACTTACTACAC	3	130	0
TGCGTCTTAAAAAAAAATTTTAAAGGAAAATA	4	195	1
TTTTAAAGGAAAATAAAGTTTAAGTCGCGCTG	4	212	1
CTCGGACACAAAATAAAGTTTATGTGTAAGAG	4	263	1
TTTTTATTGTTGAAAAAAATTAGTCTCTTTTA	2	53	1
 TATTAGTTCACAAAAATAATAAGGAGGAAAA	5	9	1
TCACTTATTTATAAAAAATATATAATACCTTA	3	28	1
TATTAGTATAATATAAAATATATAAATAAGCA	0	47	0
TTTTTCAACAATAAAAATTTTTATAATATACA	2	38	0
TTTTTTTGCAAAAAAAGCTTTATAATAAAATA	3	147	1
 TTTTGTATTATATAAGAAATAGTTTGCAATT	1	60	0
ACACGAATTGATATATACTTTACGTGCATGGA	4	143	1
GTTTGCAATTTGAAATATATTAAAGGACTGAT	1	38	0
      AAATTCAAAAACAATTTAATTTAATA	0	4	1
AATAATAAGGAGGAAAATATTAGCTTTAGAAT	5	24	1
TTTCCTTTTTAAAAAAAGAATGATTCTGAAAA	5	122	0
          * ***** ****
MAP Score: 13.9274