AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons029_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238504
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0478	29	ATP synthase F1, subunit epsilon (atpC)
#1	HI0483	49	ATP synthase F0, subunit b (atpF)
#2	HI0484	55	ATP synthase F0, subunit c (atpE)
#3	HI0485	36	ATP synthase F0, subunit a (atpB)
#4	HI0485.1	125	H. influenzae predicted coding region HI0485.1
#5	HI0486	139	glucose-inhibited division protein (gidB)

Motif 1
         TTTGTTCTCCTTCAAATGACTTGAAGT	0	12	0
GCTAAAACTTAACTTCTATTGGAGAAAATT      	2	35	1
   CTTTGGGTTATTCTTCTTCAGAACAAAGGATCG	3	7	1
ACAAATAGATAAATTATTTTCTAAAAGTGTGATTTA	4	16	1
TGCTGGCTTTAGATTCAACTTAAAAACACATAAAAA	4	60	0
CGGCGGGCTAAAATTATTTTGTAAAAGTG       	4	106	1
AGGTGCATTCAATTTATGGTGTAAAACTGGACATTG	5	19	1
      ATTTATTATCTCTTTGAAAAATTACGCTAT	5	119	0
          *  ****  *  ****
MAP Score: 9.02053

Motif 2
ACTTCAAGTCATTTGAAGGAGAACAAA      	0	12	1
CCTTATTTGCTTATCAACGTAAAACAAGCATAG	1	13	1
AAAACTTAACTTCTATTGGAGAAAATT      	2	38	1
CGATCCTTTGTTCTGAAGAAGAATAACCCAAAG	3	10	0
AATAGATAAATTATTTTCTAAAAGTGTGATTTA	4	19	1
TTTTTATGTGTTTTTAAGTTGAATCTAAAGCCA	4	60	1
CGGGCTAAAATTATTTTGTAAAAGTG       	4	109	1
TGCATTCAATTTATGGTGTAAAACTGGACATTG	5	22	1
ATTTACCGCACTTTTAAGTAAAATAGCGTAATT	5	97	1
          ** *  *******
MAP Score: 8.08789

Motif 3
 TCACTTCAAGTCATTTGAAGGAGAACAAA      	0	9	1
  TCACCTTATTTGCTTATCAACGTAAAACAAGCAT	1	8	1
GGGCTAAAACTTAACTTCTATTGGAGAAAATT    	2	33	1
AATCGATCCTTTGTTCTGAAGAAGAATAACCCAAAG	3	10	0
AATAGATAAATTATTTTCTAAAAGTGTGATTTATAT	4	19	1
CACTTTTTATGTGTTTTTAAGTTGAATCTAAAGCCA	4	57	1
CGGGCTAAAATTATTTTGTAAAAGTG          	4	109	1
ATTACGCTATTTTACTTAAAAGTGCGGTAAATTTCC	5	93	0
GTAAAATAGCGTAATTTTTCAAAGAGATAATAAAT 	5	114	1
          **  *** ***  * *
MAP Score: 4.87033

Motif 4
TATCAACGTAAAACAAGCATAGTAAGGAGGACGTT    	1	24	1
CTAGGGCTAAAACTTAACTTCTATTGGAGAAAATT    	2	30	1
ACAAATAGATAAATTATTTTCTAAAAGTGTGATTTATAT	4	16	1
AGTGTGATTTATATAACACTTTTTATGTGTTTTTAAGTT	4	41	1
CGGCGGGCTAAAATTATTTTGTAAAAGTG          	4	106	1
AGGTGCATTCAATTTATGGTGTAAAACTGGACATTGATT	5	19	1
TAAGTAAAATAGCGTAATTTTTCAAAGAGATAATAAAT 	5	111	1
          *   **   * * ** ***
MAP Score: 4.43838