AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons019_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237959
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0212	44	GTP cyclohydrolase II (ribA)
#1	HI0291	74	H. influenzae predicted coding region HI0291
#2	HI0292	76	mercuric ion scavenger protein (merP)
#3	HI0764	218	3,4-dihydroxy-2-butanone 4-phosphate synthase (ribB)
#4	HI0900	100	glutamate 5-kinase (gamma-glutamyl kinase) (proB)
#5	HI0901	80	conserved hypothetical protein
#6	HI0938	200	H. influenzae predicted coding region HI0938
#7	HI0942	45	exodeoxyribonuclease V, gamma chain (recC)
#8	HI0943	54	conserved hypothetical protein
#9	HI1301	75	carbonic anhydrase, putative
#10	HI1302_HI1303	147	HI1302: asparaginyl-tRNA synthetase (asnS), HI1303: riboflavin synthase, beta chain (ribH)
#11	HI1613	43	riboflavin synthase, alpha chain (ribE)

Motif 1
AATAACACCCTTTTATGGAGAATTATCT    	8	36	1
AACACTATATTTTTATGGAAAATTTCCTTCAT	10	100	1
CTTGAGCTATTTTTATAGGAAAAATTTAAGGT	5	49	1
CTACCCATTCATTTATGGTTAAAGTGCGGTGG	6	162	1
AGTGCGGTCAATTTTTGGCAAATTTTTCCTGC	3	21	1
ACTGCTAAAAATTTTTAGAAAAGGAAAAAATT	11	21	1
TATAGGAAAAATTTAAGGTAAAACGATA    	5	62	1
AAATAACCTATTTTTTAGTAGAATAACACCCT	8	15	1
TTTTTTCAGAATTTTAAGGAAAGTAAA     	9	58	1
TTAGGACTCATTTTTAAGGCGATTTTATTGTT	10	55	1
GTAACGGCAAATTTTAGGGGGATTT       	4	3	0
TTCAACTAGTTATTTTGGCAAATCTCGCTATA	6	51	0
TTCCACCAGCTTTTAAAGAACAGAAAAATTCC	6	12	1
TTGTTAGTTGTTTTATTGATGAATGCGATTGG	1	43	0
GTACGGTCAATATTAAAGTTAAATTGAA    	9	6	0
TTTAAGGCGATTTTATTGTTCATAACCCGCAC	10	67	1
TAGTTGTTTTATTGATGGTTAAACTATAAACC	2	41	0
ATCTGCTGACTTTAAAAGTGAAAATCAGGACA	3	58	0
GGCGTTGTTTTTTCTAGGTTAAATCATCAAAA	7	13	1
          ********  **
MAP Score: 19.6741

Motif 2
TTCTGTTAGAATGCGCGCGTTATTTTTGTTATCAAGG	0	17	0
ACATAAGGTTAAGGTCAAGAAGTTTTTT         	2	1	0
 GAGCGTTTAAAAGTGCGGTCAATTTTTGGCAAATTT	3	9	1
TTTAAAAGTGAAAATCAGGACAATTTCGCAGGAAAAA	3	43	0
TTAAAGTCAGCAGATTTGGTGAAATTCCAAAGCCGAC	3	75	1
AATATCAGGTATAGTAACGGCAAATTTTAGGGGGATT	4	11	0
TACTATACCTGATATTAAGTGATTTTTCATTGATTTA	4	32	1
TTTAGTGATAACGTTAATGCCAATTTTAAGAACTTGG	4	65	1
TTTATGAAACAATCTTGAGCTATTTTTATAGGAAAAA	5	36	1
ATCTCGCTATAATGGCACGGAATTTTTCTGTTCTTTA	6	25	0
TCGCNAAAATCAGATCAAGTGATTTTTCTACCCATTC	6	135	1
TACTTACGCCAAAGTGCGGTCAATTTTTTCAGAATTT	9	35	1
TTTAGGACTCATTTTTAAGGCGATTTTATTGTTCATA	10	54	1
CCAACACTATATTTTTATGGAAAATTTCCTTCATTAA	10	98	1
TCATTAAGGTAAACTATCGGCAATTTTAT        	10	128	1
 AAATTTGATATACTGCTAAAAATTTTTAGAAAAGGA	11	9	1
          **  *   *  ******
MAP Score: 17.3825

Motif 3
TTTGCCAAAAATTGACCGCACTTTTAAACGCTC 	3	9	0
TGCGGTCAATTTTTGGCAAATTTTTCCTGCGAAA	3	23	1
TTCCTGCGAAATTGTCCTGATTTTCACTTTTAAA	3	46	1
AATTTCACCAAATCTGCTGACTTTAAAAGTGAAA	3	67	0
TTTATTCTCTTTCATCCAGACTTTACTGTCGGCT	3	105	0
TCAGGTATAGTAACGGCAAATTTTAGGGGGATTT	4	10	0
TTTGCCGTTACTATACCTGATATTAAGTGATTTT	4	24	1
AGTGATAACGTTAATGCCAATTTTAAGAACTTGG	4	68	1
ATGAAACAATCTTGAGCTATTTTTATAGGAAAAA	5	39	1
        ATTTCCACCAGCTTTTAAAGAACAGA	6	2	1
CGCTCCAATTTTCCACCGCACTTTAACCATAAAT	6	172	0
TAACTTTAATATTGACCGTACTTACGCCAAAGTG	9	17	1
TTCTGAAAAAATTGACCGCACTTTGGCGTAAGTA	9	35	0
TTAATATTGAATATACGCGATTTT          	10	0	0
ATTAATAAGGCTTTACCCTATTTTATTTAGGACT	10	29	1
CCTATTTTATTTAGGACTCATTTTTAAGGCGATT	10	45	1
GTTTACCTTAATGAAGGAAATTTTCCATAAAAAT	10	108	0
          **  ***  *****
MAP Score: 10.5235