AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons014_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237716
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0501	167	high affinity ribose transport protein (rbsD)
#1	HI0505	97	ribokinase (rbsK)
#2	HI0506	27	rbs repressor (rbsR)
#3	HI0821	207	galactose operon repressor (galR)
#4	HI0822	90	galactose ABC transporter, periplasmic-binding protein (mglB)
#5	HI0823	65	galactoside ABC transporter, ATP-binding protein (mglA)
#6	HI1106	111	xylose operon regluatory protein (xylR)
#7	HI1110	50	D-xylose ABC transporter, ATP-binding protein (xylG)
#8	HI1111	233	D-xylose ABC transporter, periplasmic-binding protein (xylF)
#9	HI1526	84	ADP-heptose synthase (rfaE)
#10	HI1635	274	purine nucleotide synthesis repressor (purR)

Motif 1
ACAAAATAAGAAAATAAGCAAAATTTTTTATGATT	3	89	1
GTTTTTCACAAAAATACGAAAAATTTCATCACCTA	8	24	0
ACAAACCTTTATAATAGGAAAAATTTTTAGGGATT	10	242	1
TCTCTCTATTTGAATAACCAAAATTGTGGCGATTT	9	52	0
AATTTTGTGATCAATATCCCAAATTTGAAATTTCT	0	70	1
TTCCCCTTAGATTACAACAAAAATTGATGGGAAA 	5	9	0
TGGCGATTTTACCACAACTCAAATTTACGATAAAC	9	26	0
TATCTTTTCTATTATAACTTAAATAGCAATTTCCC	6	69	1
TCGAAACGTTTCGATAAGACAAATATAGATAACAA	0	122	0
GATCATAAATAATTTACGATAAATTGAAAGCGGTT	3	144	0
TCTAGCAAGAATAATACGAAAAAATCACTTCTTTT	10	171	1
AAGACAAATATAGATAACAAAAATAGAAAAACAAC	0	107	0
AATGAAAATGATTACATAAAAAATTATGAATTTGT	4	25	0
GTTATATCACATTATGGGGCAAATTATATTTGTCC	1	30	1
AAAATATAACAATACAGGATAAAATA         	1	81	1
ACAAAATTTCTAGATAGGATAAAAAATTCTCCGAC	0	43	0
CGATTACATTAATTTATACTAAATTATTGTAAATA	3	38	1
TTTATATCCTTATCTATGGGAAATTGCTATTTAAG	6	86	0
TTCTTTCTACACAATGGGACAAATATAATTTGCCC	1	46	0
CCATAATCATTGCATAACCAAAATCGCTCATTTTG	10	108	1
AAATCACTTCTTTTTATAAAAAATTTGCAATAAAG	10	192	1
         AAAAACACCCTAAAAATTCACCGCAC	2	11	0
TTGCAAATAATCAACATAGAAAAATTAAATAACAT	8	75	0
          *  *** *  *****
MAP Score: 25.2905

Motif 2
TTTCTAGATAGGATAAAAAATTCTCCGACCAA	0	40	0
TTTGTGATCAATATCCCAAATTTGAAATTTCT	0	73	1
ATAGAAAAACAACTAAGAAATTTCAAATTTGG	0	88	0
AGACAAATATAGATAACAAAAATAGAAAAACA	0	109	0
       TCTATCTACTAAATAAGCTCGTTAT	1	3	1
CATTGTGTAGAAAGAAAAAATATAACAATACA	1	65	1
TCGTTTACATTGATAAAAAACAGGAGTCAAA 	3	9	0
TTACATTAATTTATACTAAATTATTGTAAATA	3	41	1
CTTTGTCACAAAATAAGAAAATAAGCAAAATT	3	82	1
ATGAACTAAATCATAAAAAATTTTGCTTATTT	3	100	0
CGCTTTCAATTTATCGTAAATTATTTATGATC	3	147	1
GAAAATGATTACATAAAAAATTATGAATTTGT	4	25	0
TCCCCTTAGATTACAACAAAAATTGATGGGAA	5	11	0
TTCATCACCTAGAGAGGAAAATGTT       	8	3	0
TTTTTCACAAAAATACGAAAAATTTCATCACC	8	26	0
CAAATAATCAACATAGAAAAATTAAATAACAT	8	75	0
GGGGCGTAGTTTATCGTAAATTTGAGTTGTGG	9	18	1
AAAACTGCGGTGATAATAAAAAGTTGGTTTGA	10	26	1
ACGACAACAGACATACTAAAAACAACCATAAT	10	83	1
TTTTTTATGAGGAGAACAAAATGAGCGATTTT	10	127	0
TTTGTTCTCCTCATAAAAAATAACGCAGACAT	10	139	1
CTAGCAAGAATAATACGAAAAAATCACTTCTT	10	172	1
TCACTTCTTTTTATAAAAAATTTGCAATAAAG	10	195	1
CAAACCTTTATAATAGGAAAAATTTTTAGGGA	10	243	1
          * **** *****
MAP Score: 19.5768

Motif 3
TCCGATTCCGATTGAATGTAAATTTGGTCGGAGA	0	17	1
AAAATAGAAAAACAACTAAGAAATTTCAAATTTG	0	89	0
TCCCATTGTGTAGAAAGAAAAAATATAACAATAC	1	62	1
AAATATAACAATACAGGATAAAATA         	1	82	1
CAAAATAAGAAAATAAGCAAAATTTTTTATGATT	3	90	1
ATCATAAATAATTTACGATAAATTGAAAGCGGTT	3	144	0
TATAGATTATAACAAGGAAAAAGTT         	3	192	1
TGATTACATAAAAAATTATGAATTTGTGATCCAT	4	18	0
ATCGTAATTAATCTATGAGCAAATTTGCAAAAAT	4	57	0
CTCATAGATTAATTACGATAATTTATTT      	4	72	1
TTTTGTTGTAATCTAAGGGGAAGTGGATCTTCCC	5	22	1
CAACCTCTTTAAAAAGGGGAAGATCCACTTCCCC	5	38	0
TATTTAAGTTATAATAGAAAAGATATTTAGCTTC	6	60	0
TTATATCCTTATCTATGGGAAATTGCTATTTAAG	6	86	0
TTTTTCACAAAAATACGAAAAATTTCATCACCTA	8	24	0
AAATAACATAATTGATGAAAAGTTAGTTTTTCAC	8	50	0
GCAAATAATCAACATAGAAAAATTAAATAACATA	8	74	0
AAAAAAGGCTTTCAATTATAAAATCTTTCTCCAT	8	146	0
AGCCTTTTTTAAAGTGTGAAAACTAACAACTGGA	8	170	1
CACAACTCAAATTTACGATAAACTACGCCCCTAA	9	15	0
AAAAAGTTGGTTTGATTAAAAGATTGAAAGTGCA	10	43	1
CTAGCAAGAATAATACGAAAAAATCACTTCTTTT	10	172	1
ACAAACCTTTATAATAGGAAAAATTTTTAGGGAT	10	242	1
          **  * ****** *
MAP Score: 11.1033

Motif 4
AAATTTGGTCGGAGAATTTTTTATCCTATCT	0	36	1
AAATTTCTTAGTTGTTTTTCTATTTTTGTTA	0	97	1
ATCCTGTATTGTTATATTTTTTCTTTCTACA	1	70	0
     AGTGCGGTGAATTTTTAGGGTGTTTT	2	5	1
AAGAAAATAAGCAAAATTTTTTATGATTTAG	3	96	1
TCAATTTATCGTAAATTATTTATGATCAAAA	3	152	1
ATCACAAATTCATAATTTTTTATGTAATCAT	4	22	1
GATTAATTACGATAATTTATTT         	4	78	1
TTATCTTGAAGCTAAATATCTTTTCTATTAT	6	53	1
CTCTCTAGGTGATGAAATTTTTCGTATTTTT	8	19	1
ATTTTTCTATGTTGATTATTTGCAACTGTGG	8	85	1
TATAAAAAGAAGTGATTTTTTCGTATTATTC	10	179	0
CATCTTTATTGCAAATTTTTTATAAAAAGAA	10	199	0
TTTATAATAGGAAAAATTTTTAGGGATTTAA	10	249	1
          * *********
MAP Score: 7.40001