AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons007_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237262
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0007	300	formate dehydrogenase, beta subunit (fdxH)
#1	HI0009	69	fdhE protein (fdhE)
#2	HI0090	300	conserved hypothetical protein
#3	HI0345	300	ferredoxin-type protein (napG)
#4	HI0563	153	transcriptional regulatory protein (asnC)
#5	HI0643	32	biotin sulfoxide reductase (bisC)
#6	HI0644	148	cytochrome C-type protein (yecK)
#7	HI0747	203	NADH dehydrogenase (ndh)
#8	HI1044	111	conserved hypothetical protein
#9	HI1047_HI1048	253	HI1047: anaerobic dimethyl sulfoxide reductase, chain A (dmsA), HI1048: H. influenzae predicted coding region HI1048
#10	HI1068	43	nitrite reductase, cytochrome C-type protein (nrfB)
#11	HI1069	161	nitrite reductase, cytochrome C552 (nrfA)
#12	HI1556	59	2-hydroxyacid dehydrogenase
#13	HI1560	22	H. influenzae predicted coding region HI1560
#14	HI1561	106	peptide chain release factor 1 (prfA)

Motif 1
GTCAATTTTAACCGCACTTTTTCTTTTTCA	1	20	0
GTTAAAATTGACCGCACTTTTTATTATAAA	1	38	1
ATGAAAAATAACCGCACTTTATCCGTAATC	2	136	0
GTGTAAACTAACCGCACTTTTTTATAAAGG	2	273	1
TTCCACTTTTACCGCACATTTTTTGAAGTC	3	214	0
GTAAAAATCAACCGCACTTTATTTTCTCCC	3	263	1
CTATTTCAGCACCGTTCTTTGTTATCGAAT	7	16	0
CAAAAAAATAACCGCACTTTGATATATAAG	7	84	1
CATAAAAATAACCGCACTTATATATCAAAG	7	100	0
TGAAAAATGCACCGCACTTTTTAGTGCAAA	10	11	1
GTCAAAATTAACCGCACTTTTGATGAAAT 	12	9	0
GTTAATTTTGACCGCACTTTGTATATAAAA	12	27	1
          **********
MAP Score: 57.715

Motif 2
GAATAGCGGGTTTTTTTATAAATTTAAAAA     	2	5	0
GTTAGGGTTGTTTTTTATTATTTTATTGGA     	6	128	1
AATATACCTCTTTTTGAGTATTTTAAAAGATAAGC	11	68	1
TAATTAACTCGTTTTAGTTATTTTTCAATCTGACT	9	212	1
GTATATTGTTGTTTTAAATAAATTAAGGCGGTATA	11	40	0
CCATATCGCCTTTTTGGATGCCTTTTTCTGCCGCT	0	20	0
AGTGCGGTTATTTTTCATTGTGTTTTATCTTGAAA	2	148	1
GTGCGGTTGATTTTTACATGGTTTTTACGCAGCCT	3	245	0
AGTGCGGTTATTTTTATGAAAGTTTTCCGCCCTGT	7	112	1
AAGTGACAAATTTTTCAGAAATTTTCTTAGTCAAT	2	231	1
TACGCCTCAATTTTTAGAAACGTTAATTAGTAATA	8	31	1
CCTCCTTTAGATTTTATTTAATTTTTTCACAATGA	4	121	0
TTATATAGTGTTTTTCTTCAGCTTATAACATTTTT	6	31	1
GTAGATTGATGTTTTAATAAACTTTGGAATAACAA	9	102	0
TGAATCGCGGGTTTTCTGTATCTTGTTTTTGCTGC	2	43	1
CGCCGATTTTATTTTCGGTGACTTACAA       	14	88	1
AAAACTTTTTTCTTTTGGTATCTTACGCTTGA   	11	139	1
TGCGGTTATTTTTTTGAGTTATTTTAAGTTGATAT	7	65	0
TTAATGTAACATTTTTAACAATTTAAACTTTTAGG	7	170	1
TCGTTGTTATGTTATCATTACATTAATGTAACATT	7	148	1
TCTCAGACGCTTTATTTGTGATTTACCCA      	14	4	0
AGGAGTAATATTTTTGAGTATTATTCAGTAAATAA	4	30	1
          *****   **  ***
MAP Score: 16.8332

Motif 3
CATTCTTGGTAAATATTGAAAAAGTTGGGGAGG	0	271	1
      GCTGAAATCCTGAAAAAGAAAAAGTGC	1	4	1
      TTTTTAAATTTATAAAAAAACCCGCTA	2	4	1
TCAAGATAAAACACAATGAAAAATAACCGCACT	2	148	0
TCATTGTGTTTTATCTTGAAAAATGAATGCGTA	2	162	1
TGACTAAGAAAATTTCTGAAAAATTTGTCACTT	2	231	0
AAATGTGCGGTAAAAGTGGAAAAGGCTGCGTAA	3	223	1
GGCTGCGTAAAAACCATGTAAAAATCAACCGCA	3	246	1
ATTTACTGAATAATACTCAAAAATATTACTCCT	4	30	0
ATCATCTAATTCATTGTGAAAAAATTAAATAAA	4	111	1
 TGAATGAATTAACTATCTAAAACGAGGCTGAA	5	9	1
   TCCAATAAAATAATAAAAAACAACCCTAAC	6	128	0
ATCAACTTAAAATAACTCAAAAAAATAACCGCA	7	67	1
CTAAAAGTTTAAATTGTTAAAAATGTTACATTA	7	171	0
TCCCCCACAGTCAGATTGAAAAATAACTAAAAC	9	222	0
TTATCTTTTAAAATACTCAAAAAGAGGTATATT	11	68	0
          ***   *******
MAP Score: 12.462

Motif 4
CGGTCAATTTTAACCGCACTTTTTCTTTTTCAGGATTT	1	14	0
TGCGGTTAAAATTGACCGCACTTTTTATTATAAAAGTG	1	34	1
AATTTCTGAAAAATTTGTCACTTTCTGTTTGACAAGCT	2	216	0
CCGCACATTTTTTGAAGTCGGTTTCTTTTGAAATTGGG	3	195	0
CCATGTAAAAATCAACCGCACTTTATTTTCTCCCATCA	3	259	1
          TTCAGCCTCGTTTTAGATAGTTAATTCA	5	14	0
TTTCTTCAGCTTATAACATTTTTTCTTGAGAAATATCA	6	43	1
AACGGTGCTGAAATAGCACCGTTTTTGTTGTTCTAATA	7	30	1
TTATGAAAGTTTTCCGCCCTGTTTCGTTGTTATGTTAT	7	125	1
GGCGTATAGCATACGCCTCAATTTTTAGAAACGTTAAT	8	20	1
CAAAGATTATAATTAACTCGTTTTAGTTATTTTTCAAT	9	203	1
   ATGAAAAATGCACCGCACTTTTTAGTGCAAACTAG	10	7	1
GGCGGTATAAAACCGCCTTAATTTTGAGTATTATTATC	11	11	0
GGCGGTTTTATACCGCCTTAATTTATTTAAAACAACAA	11	32	1
TAAAACAACAATATACCTCTTTTTGAGTATTTTAAAAG	11	59	1
TGCGGTCAAAATTAACCGCACTTTTGATGAAAT     	12	5	0
TGCGGTTAATTTTGACCGCACTTTGTATATAAAAAAGG	12	23	1
          TAATTGCTCCTTTTTTATATACAAAGTG	12	41	0
GAAATTAAGAATCTCAGACGCTTTATTTGTGATTTACC	14	12	0
AAATCGGCGTATTCTAGCCGATTTTAGGGAAAATTGAC	14	59	0
          **   ** *  *** * *
MAP Score: 11.6977

Motif 5
       GCGAAAAATTAGCGGCAGAAAAAGG	0	3	1
GTAAATATTGAAAAAGTTGGGGAGGCATAAT 	0	279	1
AAGTGCGGTTAAAATTGACCGCACTTTTTATT	1	31	1
TTAAATTTATAAAAAAACCCGCTATTCAGTTG	2	13	1
AAACACAATGAAAAATAACCGCACTTTATCCG	2	141	0
TTTCCTTTATAAAAAAGTGCGGTTAGTTTACA	2	274	0
AGAAAGTGGTAAATACTAAGCCACGAGGTGGT	3	117	0
ACCGACTTCAAAAAATGTGCGGTAAAAGTGGA	3	211	1
AAAACCATGTAAAAATCAACCGCACTTTATTT	3	255	1
AAAATTAAATAAAATCTAAAGGAGGAAGTTTT	4	131	1
ATAAAATAATAAAAAACAACCCTAACTACTTA	6	122	0
GTGATTCGATAACAAAGAACGGTGCTGAAATA	7	13	1
AAATAACTCAAAAAAATAACCGCACTTTGATA	7	76	1
AAACTTTCATAAAAATAACCGCACTTATATAT	7	105	0
AACGTTTCTAAAAATTGAGGCGTATGCTATAC	8	23	0
       ATGAAAAATGCACCGCACTTTTTAG	10	3	1
AATAATACTCAAAATTAAGGCGGTTTTATACC	11	14	1
AAGTGCGGTCAAAATTAACCGCACTTTTGATG	12	14	0
GATTTTAGGGAAAATTGACAGCGAAAAGGAAA	14	46	0
GTCACCGAAAATAAAATCGGCGTATTCTAGCC	14	78	0
          *****  *****
MAP Score: 10.9997

Motif 6
CAGAATACAAAACATTCTTGGTAAATATTGAAAAA	0	259	1
CCTGAAAAAGAAAAAGTGCGGTTAAAATTGACCGC	1	18	1
ATTGACTAAGAAAATTTCTGAAAAATTTGTCACTT	2	231	0
TCTTAGTCAATAAATTTCGTGTAAACTAACCGCAC	2	255	1
CCGACTTCAAAAAATGTGCGGTAAAAGTGGAAAAG	3	212	1
GTAAAAGTGGAAAAGGCTGCGTAAAAACCATGTAA	3	232	1
AAGTAAATAAAATACTTGAAATAAAATCATTATTT	4	59	0
ATTCATTGTGAAAAAATTAAATAAAATCTAAAGGA	4	119	1
AAGCTGAAGAAAAACACTATATAAATCAATAAATA	6	20	0
ATATCAACTTAAAATAACTCAAAAAAATAACCGCA	7	65	1
AGTTAAACTTAACATATTAGATAAACTAACACGCC	9	33	1
TCAATCTACTAAAATACCCTATAAATAATATACCT	9	128	1
      TGGGTAAATCACAAATAAAGCGTCTGAGA	14	4	1
          ****   *  *****
MAP Score: 2.83285