AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_operons073_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248265
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	tenA	248	transcriptional regulator
#1	thiD	148	phosphomethylpyrimidine kinase
#2	ywbI	105	alternate gene name: ipa-24d; similar to transcriptional regulator (LysR family)

Motif 1
AGGATTCGTGTTAATATAGAGGTGCAGAACA	0	24	1
GCAGAACAATTCAATATGTATTCGTTTAACC	0	47	1
CTACCTAGTTTTCTTATGTAGCATTTTACGA	1	23	1
TGTCAAATGATTCCTATAGATCTTCTATATA	1	68	1
CTATAGATCTTCTATATATTGTGATACAGAG	1	81	1
ATAGTTAGATTTTCTCTGTATCACAATATAT	1	94	0
GTTTTGTCTTTCATTATAGTTAGATTTTCTC	1	109	0
GTACATAAGGTCTCTCTATAGGTAAAATATA	2	36	1
CTTCTTATTCTTAATATATATTTTACCTATA	2	52	0
AAGTATTCCTTTTGTCTATAGAAAGGGTGAA	2	80	1
          *** *******
MAP Score: 4.87065

Motif 2
CACTAGGGGTGTCCTTCATAAGGGCTGAGAT	0	77	1
GTGACTTTTAGACCCTCATAACTTGAACAGG	0	114	1
AACAGGTTCAGACCTGCGTAGGGAAGTGGAG	0	139	1
AATCTCAACGGGCTTTCGTAAAATGCTACAT	1	38	0
ATCATGTTTTGTCTTTCATTATAGTTAGATT	1	114	0
          * *********
MAP Score: 3.19037

Motif 3
TAAGGATTCGTGTTAATATAGAGGTGCAGAA	0	22	1
TCATTCCCCCTCTGAAAATAAAAAAACCACT	0	224	0
CTATAGATCTTCTATATATTGTGATACAGAG	1	81	1
ACAGAGAAAATCTAACTATAATGAAAGACAA	1	106	1
GTACATAAGGTCTCTCTATAGGTAAAATATA	2	36	1
TACTTCTTATTCTTAATATATATTTTACCTA	2	54	0
 GCGCTTCACCCTTTCTATAGACAAAAGGAA	2	85	0
          *** *******
MAP Score: 2.84464

Motif 4
GCAGAACAATTCAATATGTATTCGTTTAAC	0	47	1
ATATAGAAGATCTATAGGAATCATTTGACA	1	68	0
CTATAGATCTTCTATATATTGTGATACAGA	1	81	1
ATAAGGTCTCTCTATAGGTAAAATATATAT	2	40	1
CTTCTTATTCTTAATATATATTTTACCTAT	2	53	0
CTTCACCCTTTCTATAGACAAAAGGAATAC	2	82	0
          **********
MAP Score: 2.52767

Motif 5
TGCAGAACAATTCAATATGTATTCGTTTAA	0	46	1
CCTACCTAGTTTTCTTATGTAGCATTTTAC	1	22	1
CCTATAGATCTTCTATATATTGTGATACAG	1	80	1
TGTTTTGTCTTTCATTATAGTTAGATTTTC	1	111	0
GTCTTGAACCTCCATCATGTTTTGTCTTTC	1	128	0
 ATTGATGCCTCCCTTATATACTTATTGTA	2	9	1
ATACTTCTTATTCTTAATATATATTTTACC	2	56	0
ATAAGAAGTATTCCTTTTGTCTATAGAAAG	2	75	1
          **********
MAP Score: 1.86875