AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237063
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0613	72	fuculokinase (fucK)
#1	HI0614	181	L-fucose isomerase (fucI)
#2	HI0615_HI0616	197	HI0615: L-fucose operon activator (fucR), HI0616: ATP-dependent helicase (hepA)
#3	HI0618	26	glp protein, putative
#4	HI0619	29	glycerol-3-phosphate regulon repressor (glpR)
#5	HI0685	292	anaerobic glycerol-3-phosphate dehydrogenase, subunit A (glpA)
#6	HI0690	229	glycerol uptake facilitator protein (glpF)
#7	HI1009_HI1010	158	HI1009: glycerol-3-phosphate regulon repressor (glpR), HI1010: 3-hydroxyisobutyrate dehydrogenase, putative
#8	HI1017	237	glycerol uptake facilitator protein (glpF)
#9	HI1024	49	hexulose-6-phosphate synthase, putative
#10	HI1027	58	L-xylulose kinase (lyx)
#11	HI1028	30	conserved hypothetical protein
#12	HI1030	71	conserved hypothetical transmembrane protein
#13	HI1031	175	conserved hypothetical protein
#14	HI1112	233	xylose isomerase (xylA)

Motif 1
AAGAAAGTAAAAAAAATCAAAAATGTGAAGTGTT	5	102	1
GTTTTTCACAAAAATACGAAAAATTTCATCACCT	14	194	1
TTATCACTAAAATTAACAAAAAATAACATTTTTT	7	98	0
TTTTGACCGAAAATTACTAAAAATTGAAAGAATC	1	23	1
CTTGAAAAGAAACTCACAAAAAATTGACCGCACT	2	70	1
CGAATCATAAAAGAAAATAAAAAATAAGAAAGTA	5	77	1
AAGGGAAGAGAATTTATTAAAAAAGAATACGGAG	6	155	0
GCAAATAATCAACATAGAAAAATTAAATAACATA	14	145	1
TTCTATATCGTAGAAACTAAAAATCTACTCTAAC	6	54	1
GGCTGGATTTTACATAATAAAAATCCAGCCCATA	10	16	1
CTAGATCACAAAATCAGTAAAATTATTTTAACAT	13	46	1
TAAATAACATAATTGATGAAAAGTTAGTTTTTCA	14	168	1
     TACAGAAAATCCGAAAAATTGCCACCAAG	8	5	1
AAGCTCAGTCAATAAATGTAAAATAAATAAATTA	13	93	0
TACGTTTCATAATTTACAAAAATAAGAAAGCTCA	13	120	0
CTCTTAATTTTATATAGTAAAATTACGTTTCATA	13	143	0
CTAGATCACAGAATGATAAAAAATGTTATTTTTT	7	81	1
GCCAAGTCCTAACACCATAAAAAATGCTGTTCCC	8	211	0
ATGTAAGAAAAAATAATATAAAAAGTGTAATCAT	5	247	0
CACTCCTATCTAGATATAAAAAGAGTGCTAGAGA	8	136	0
TATCGGCTAATATACAGATAAATTTAGTTAAGAT	7	27	0
          ** * *  ******
MAP Score: 21.6346

Motif 2
TTGACCGAAAATTACTAAAAATTGAAAGAA	1	25	1
AACTGCGAGCATCACAAAAATTGACTATAT	1	77	0
TGAAAAGAAACTCACAAAAAATTGACCGCA	2	72	1
TGTGATATTGATCACAATAATTTTCGCATT	5	162	0
TGTGATCAATATCACAAAATCGCTTTCTTT	5	176	1
TTACCCCCGATTCCCAAAATGTAAGAAAAA	5	269	0
TGAGATCTAGATCACAGAATGATAAAAAAT	7	75	1
ATCACTAAAATTAACAAAAAATAACATTTT	7	100	0
ATAACGTTTTATCACTAAAATTAACAAAAA	7	110	0
          TTCACAATATGAAATATTAT	13	0	1
ATGAAATATTATCACAAGAAAATAGGATCT	13	18	1
TAGGATCTAGATCACAAAATCAGTAAAATT	13	40	1
CGTTTCATAATTTACAAAAATAAGAAAGCT	13	122	0
AAGTTAGTTTTTCACAAAAATACGAAAAAT	14	188	1
          **********
MAP Score: 16.2073

Motif 3
TGACCGATTCTTTCAATTTTTAGTAATTTTCGGTCAAAA	1	23	0
TGCAACAAAATTTCATTTCTTACTGTTTTCCTTATCATT	1	108	1
GTCACCCCAATATAATTTATCCTTGGATTTTCAATATAC	2	119	1
TTTCTTATTTTTTATTTTCTTTTATGATTCGCAAATCCC	5	69	0
CATTTTTGATTTTTTTTACTTTCTTATTTTTTATTTTCT	5	88	0
ACACTTTTTATATTATTTTTTCTTACATTTTGGGAATCG	5	253	1
AAACACTCCGTATTCTTTTTTAATAAATTCTCTTCCCTT	6	150	1
TGATAAAAAATGTTATTTTTTGTTAATTTTAGTGATAAA	7	94	1
CATATTGATTTATAAATAATTTATTTATTTTACATTTAT	13	77	1
TTGACTGAGCTTTCTTATTTTTGTAAATTATGAAACGTA	13	115	1
        TTTTTCCTCTCTTAATTTTATATAGTAAAAT	13	154	0
GGCTTTCAATTATAAAATCTTTCTCCATTATTACGTTTT	14	79	1
GTTATTTAATTTTTCTATGTTGATTATTTGCAACTGTGG	14	137	0
          * *  * * **  *  ***
MAP Score: 11.8762

Motif 4
TCATTATGTTTTTGACCGCACTTTTTTATAAAA	0	22	0
CATAATGATTTTTGACTGCGCTGAGGAGAGTTT	0	47	1
CTCACAAAAAATTGACCGCACTTTTAGGAAGAT	2	82	1
TGTTGTTAATTTTGGCCGCACTTCCCTACAATG	5	217	1
TTTTTAATAAATTCTCTTCCCTTTACTTAGGGA	6	166	1
CACTCTTCATTTCAACCGCACTTCTAAGGAGTG	6	202	1
TTTTACATTTATTGACTGAGCTTTCTTATTTTT	13	104	1
          TTTTTCCTCTCTTAATTTTATAT	13	162	0
       AACATTTTCCTCTCTAGGTGATGAAA	14	217	0
          ***  **** ***
MAP Score: 9.56111

Motif 5
TCATTATGTTTTTGACCGCACTTTTTTATA	0	25	0
AAATGACCATTTTGACCGAAAATTACTAAA	1	14	1
AGGAAATGTATATGACCGATTCTTTCAATT	1	44	0
CTCACAAAAAATTGACCGCACTTTTAGGAA	2	82	1
CTTTACACCGTTTGAGCGAATGCGAAAATT	5	144	1
TGTTGTTAATTTTGGCCGCACTTCCCTACA	5	217	1
CACTCTTCATTTCAACCGCACTTCTAAGGA	6	202	1
TTATCTGTATATTAGCCGATACAATAAATT	7	40	1
          **********
MAP Score: 4.1595

Motif 6
CCATAATATAAAACGAATCACATTTGTGATAATC	12	34	1
TTATTATGTAAAATCCAGCCTATTGA        	10	2	0
AAGATTTGTGAAACACTTCACATTTTTGATTTTT	5	113	0
CTAGGTGATGAAATTTTTCGTATTTTTGTGAAAA	14	196	0
TACATAATAAAAATCCAGCCCATAAAAAACTAAG	10	26	1
GGCTATTTCAAAACACTCCGTATTCTTTTTTAAT	6	140	1
AATCTCGACTAAATCCACCGTATAGGGAAAAGAG	2	173	1
AACTCACAAAAAATTGACCGCACTTTTAGGAAGA	2	80	1
AGTGCGGCCAAAATTAACAACATTTTGAGTGTAA	5	205	0
AGCATCACAAAAATTGACTATATTTAAGGAAATG	1	66	0
TACTTAGGGAAAACACTCTTCATTTCAACCGCAC	6	189	1
TGTGTCATCTAAATTTACCCTTTTGAAACAGTAA	5	35	1
CCACAGTTGCAAATAATCAACATAGAAAAATTAA	14	137	1
          ****  * * ****
MAP Score: 3.64388

Motif 7
TCTTTCAATTTTTAGTAATTTTCGGTCAAAA	1	23	0
CAAAATTTCATTTCTTACTGTTTTCCTTATC	1	113	1
ATCATTTTTCTTTCACACTCTAATTCAATGA	1	141	1
        AATTATTCTCTTTCTGATTTACA	2	2	1
GCCCCCAAGTTTTATCAATGTAAATCAGAAA	2	20	0
TCTCCAACTTTTTAATTATGTGTCATCTAAA	5	17	1
TCATCTAAATTTACCCTTTTGAAACAGTAAG	5	39	1
TTCTTATTTTTTATTTTCTTTTATGATTCGC	5	76	0
TTTTTTTTACTTTCTTATTTTTTATTTTCTT	5	87	0
ATTACACTTTTTATATTATTTTTTCTTACAT	5	250	1
TATATTATTTTTTCTTACATTTTGGGAATCG	5	261	1
TAGAGTAGATTTTTAGTTTCTACGATATAGA	6	55	0
ATAAAAAATGTTATTTTTTGTTAATTTTAGT	7	96	1
GGTGGCAATTTTTCGGATTTTCTGTA     	8	5	0
CAATGCACCATTACGCATTGTCGGGCTAGAT	8	53	1
ACTCCATCATTTATTCAATTTCAGCAATACA	8	95	0
GGTTGATATTTTACATAATCTTCACTCCTAT	8	161	0
TGGGCTGGATTTTTATTATGTAAAATCCAGC	10	17	0
TGTGATAATATTTCATATTGTGAA       	13	3	0
TAAAATAATTTTACTGATTTTGTGATCTAGA	13	45	0
TTATAAATAATTTATTTATTTTACATTTATT	13	86	1
TTGACTGAGCTTTCTTATTTTTGTAAATTAT	13	115	1
TAAAATTACGTTTCATAATTTACAAAAATAA	13	129	0
TGAAACGTAATTTTACTATATAAAATTAAGA	13	145	1
         TTTTTCCTCTCTTAATTTTATA	13	163	0
AGTTGTTAGTTTTCACACTTTAAAAAAGGCT	14	52	1
TTCTCCATTATTACGTTTTTTCACAACTGTG	14	99	1
TGTTATTTAATTTTTCTATGTTGATTATTTG	14	146	0
TTTTCATCAATTATGTTATTTAATTTTTCTA	14	159	0
TGATGAAATTTTTCGTATTTTTGTGAAAAAC	14	194	0
          **** ******
MAP Score: 3.5556

Motif 8
AAGTGCGGTCAAAAACATAATGATTTTTGACTGC	0	32	1
ATTTTGACCGAAAATTACTAAAAATTGAAAGAAT	1	22	1
GTGTGAAAGAAAAATGATAAGGAAAACAGTAAGA	1	125	0
TAGATGACACATAATTAAAAAGTTGGAGAAAAAA	5	12	0
ATCATAAAAGAAAATAAAAAATAAGAAAGTAAAA	5	80	1
AAAAAATAAGAAAGTAAAAAAAATCAAAAATGTG	5	95	1
AAGTGCGGCCAAAATTAACAACATTTTGAGTGTA	5	206	0
TTTTATCACTAAAATTAACAAAAAATAACATTTT	7	100	0
     TACAGAAAATCCGAAAAATTGCCACCAAG	8	5	1
TGGATTTTACATAATAAAAATCCAGCCCATAAAA	10	19	1
TCTAGATCACAAAATCAGTAAAATTATTTTAACA	13	45	1
AAATTATTTATAAATCAATATGTTAAAATAATTT	13	65	0
CAATAAATGTAAAATAAATAAATTATTTATAAAT	13	84	0
ATAATTTACAAAAATAAGAAAGCTCAGTCAATAA	13	112	0
ACAGTTGCAAATAATCAACATAGAAAAATTAAAT	14	139	1
CAACATAGAAAAATTAAATAACATAATTGATGAA	14	154	1
GTTTTTCACAAAAATACGAAAAATTTCATCACCT	14	194	1
          ***** ** **  *
MAP Score: 0.787203