AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_operons025_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238308
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0030	51	lipoprotein, putative
#1	HI0033	53	conserved hypothetical protein
#2	HI0034	124	conserved hypothetical protein
#3	HI0081	141	conserved hypothetical protein
#4	HI0271	78	conserved hypothetical protein
#5	HI0272	23	orotate phosphoribosyltransferase (pyrE)
#6	HI0273	300	ribonuclease PH (rph)
#7	HI0274	300	glutamyl-tRNA synthetase (gltX)
#8	HI0454	54	conserved hypothetical protein
#9	HI0457	69	conserved hypothetical protein
#10	HI0458	70	stationary phase survival protein SurA, putative
#11	HI0459	131	pyrimidine operon regulatory protein (pyrR)
#12	HI0549	169	dimethyladenosine transferase (ksgA)
#13	HI1354	300	glutaminyl-tRNA synthetase (glnS)
#14	HI1603	207	conserved hypothetical protein
#15	HI1604	24	phosphate permease, putative
#16	HI1605	65	conserved hypothetical protein
#17	HI1607	62	hemM protein (hemM)
#18	HI1664	27	conserved hypothetical protein
#19	HI1665	53	H. influenzae predicted coding region HI1665
#20	HI1667	73	conserved hypothetical protein
#21	HI1668	21	tail specific protease (prc)
#22	HI1669	38	conserved hypothetical protein
#23	HI1670	183	H. influenzae predicted coding region HI1670

Motif 1
CGGTTATTTTTTACCGCACTTTACTAAAAT 	1	9	0
CGGTAAAAAATAACCGCACTTTTTAGATAAG	1	24	1
AGCGCGAAATTAACCGCGCTTTTTATGTCTA	2	27	0
ATTATAAAAATAACCGCACTTTGACTTAACA	4	48	1
CCAACTGAGCTAATCGCCCTTAATGTTGTGG	7	121	1
ACCCCTATAATAACCGCACTTTTCTTATTAA	12	139	1
TTCAAAAAACTTACCGCACTTTGTGCATTTA	13	121	1
CGGTTAAAATTAACCGCACTTTTTATTGAGA	16	14	0
CGGTTAATTTTAACCGCACTTTTGTTGTGAT	16	29	1
AATGTAAAATTAACCGCACTTTT        	18	14	1
TAAATGGTTTTGACCGCACTTTGTTTGAGAA	20	14	1
TTTATTAAAATCACCGCACTTGTTGCTTTTC	20	42	0
TTTGCCTAGTTTATCGCACTTTTTACAAAAT	23	129	0
          * *********
MAP Score: 63.1028

Motif 2
TTTCTTTAAGAAAGAAAAAATGAAA       	0	3	0
TTTCTTAAAGAAAGAATAAATGAAAAGCGTTA	0	22	1
AAAGTGCGGTAAAAAATAACCGCACTTTTTAG	1	18	1
TTCAATTTAGACATAAAAAGCGCGGTTAATTT	2	20	1
AAATCCACGCAAAAAATAAGCGCGAAATTAAC	2	44	0
AATAACATTATAAAAATAACCGCACTTTGACT	4	42	1
ATTTTAACAAAAATAAAAACTAAAGCGTGCTA	6	227	1
CGAACGATGTAATAAAAAAGCGCACTATTCTA	6	257	0
TACGACAATTAAACAAAATTTAATAAAAAGGT	7	187	0
TTAATTGTCGTAAAAATAAGCATAAAATCCGC	7	207	1
TTGACTTCTAAATAAAAAAGCGGATTTTATGC	7	226	0
  CAAAGTATCAAAAATAAAGGGGCTTAATTG	9	8	1
AAGAAAGAGAAAATAAAAAACAACAAAAGGGG	9	40	0
GTATAACGAACAAGAAAAATGGTGCAAATGCC	11	43	1
CACAAAGTATAAAGAAAATACGCCTAAAAAGC	11	78	0
GCGGAAAAGTTAAGAAAAACGGGCGGATTATA	12	15	1
GCTTTCTACGAAAGAAAAAATAATATTGTTCA	12	57	1
CACTACATCACATTAAAAAGCGGTATCGCCGT	13	23	1
AAAAACTTGCCATAAAAAACCGCCACGAAATT	13	166	0
CGTTAAAATAAAAAAATATTCGGCTATTCTAT	13	271	0
AAAAAATTTGTAAGAAAAAAGGTTTATCTTCG	14	107	0
TAAAATTTTTCAAAAAAATTTGTAAGAAAAAA	14	119	0
TTTTAACTATCAACAAAAATCGGGTAATATGC	14	146	1
   TTGATCTCAATAAAAAGTGCGGTTAATTT	16	7	1
         TAAATAAAAATTGACTCGGAA  	21	1	1
CTTTCTTTATAAATCAAAAACGTGCCATTCTA	23	19	1
          *** ***** **
MAP Score: 33.2961

Motif 3
TAAAAAATAACCGCACTTTTTAGATAAGGATGACTT   	1	27	1
GAAATTAACCGCGCTTTTTATGTCTAAATTGAAATTATT	2	14	0
GATAGAATTCCGCACCTTTATTGCTAAGTGAGAACAAA 	2	96	1
ACGCCTTAGAGCGATCATCATCGAAAGATGAGTTTTTAA	3	39	1
GCGATAATTAGGGGATTTTTTATAGAATTTAGATAAAGA	3	107	1
AAGTCAAAGTGCGGTTATTTTTATAATGTTATTTATAAT	4	36	0
TATCATGTCGCTGTCTTTTATGGGGATATAGCTCAGTTG	6	69	1
TGCTAGAATAGTGCGCTTTTTTATTACATCGTTCGAAAC	6	254	1
AAATAAAAAAGCGGATTTTATGCTTATTTTTACGACAAT	7	210	0
GCAATTAAGCCCCTTTATTTTTGATACTTTG        	9	2	0
GGGCTTAATTGCCCCTTTTGTTGTTTTTTATTTTCTCTT	9	29	1
CGCTTTTTAGGCGTATTTTCTTTATACTTTGTGCATTGA	11	77	1
CTATAATCCGCCCGTTTTTCTTAACTTTTCCGCCTAAA 	12	9	0
CTATAATAACCGCACTTTTCTTATTAAATAGTACTT   	12	143	1
CCCAGCCAGCTCCCATTTGATAGGAAATTTTGCTGTTTT	13	66	0
AAAAAACTTACCGCACTTTGTGCATTTATACATCGCCAC	13	124	1
AATTTCGTGGCGGTTTTTTATGGCAAGTTTTTACAATCT	13	166	1
AAAAAAATATTCGGCTATTCTATACAAATCTAAGGGAAA	13	255	0
CGCATATTACCCGATTTTTGTTGATAGTTAAAATTTTTC	14	140	0
TTAAAATTAACCGCACTTTTTATTGAGATCAA       	16	3	0
TAATTTTAACCGCACTTTTGTTGTGATGTTTAAGGGGAA	16	33	1
GTTAATAAGCTCGCATATTTTAAGGATTTAGTTTAATTG	17	30	0
ATTAAAATCACCGCACTTGTTGCTTTTCTCAAACAAAGT	20	31	0
      GCTTGTGGTCTTTCTTTATAAATCAAAAACGTG	23	4	1
AACAACGGATCCCGTTATGCTGAATAAATTTCACACAAA	23	89	0
GCCTAGTTTATCGCACTTTTTACAAAATTAACAACGGAT	23	118	0
          ***  **** *    *  *
MAP Score: 29.6938

Motif 4
ATCTTTATCTAAATTCTATAAAAAATCCCCTAAT	3	113	0
TCATTATAAATAACATTATAAAAATAACCGCACT	4	34	1
ATCGGATAACAAACACATAATAAAATCGTATTGA	6	16	1
TATCTTAGCGAATTTTAACAAAAATAAAAACTAA	6	216	1
CCGCTTGGTCAAACTTAGTAAAATTAAGAAAACT	7	19	1
AAAATTAAGAAAACTTTTTAGAGAAGTGGTGGGC	7	38	1
CAATTAAACAAAATTTAATAAAAAGGTATTGACT	7	180	0
ATACTATCCAAAACATTCCATCAAAGGAAACCAA	11	13	0
TTTAGGCGGAAAAGTTAAGAAAAACGGGCGGATT	12	10	1
AAAAACAGCAAAATTTCCTATCAAATGGGAGCTG	13	65	1
TTGGTAAGCTAAACATTCAAAAAACTTACCGCAC	13	106	1
AAGATTGTAAAAACTTGCCATAAAAAACCGCCAC	13	172	0
TTTTTCAAAAAAATTTGTAAGAAAAAAGGTTTAT	14	112	0
    TCAACAAAACATAGGAAATAAACT      	15	6	1
TTTTCCCCTTAAACATCACAACAAAAGTGCGGTT	16	40	0
GAACCAACAGAAATTTGTGAAAAATCAACCGCAC	22	10	0
TATGCTGAATAAATTTCACACAAAAATAACGCCA	23	79	0
GATCCGTTGTTAATTTTGTAAAAAGTGCGATAAA	23	117	1
          ******   * ***
MAP Score: 14.732

Motif 5
TAAATGAAAAGCGTTAATATTTT        	0	38	1
GAAATTAACCGCGCTTTTTATGTCTAAATTG	2	22	0
GGTTAATTTCGCGCTTATTTTTTGCGTGGAT	2	43	1
CTTATTTTTTGCGTGGATTTTGCGCAAGAGG	2	56	1
TAGCGATAATTAGGGGATTTTTTATAGAATT	3	105	1
TTAAGTCAAAGTGCGGTTATTTTTATAATGT	4	46	0
TTTTATCATGTCGCTGTCTTTTATGGGGATA	6	66	1
GTAAAGCACCTTGCTGTTTTATTATCAATAA	6	181	1
ATCAATATCTTAGCGAATTTTAACAAAAATA	6	211	1
CTAAATAAAAAAGCGGATTTTATGCTTATTT	7	220	0
ATTGCCCCTTTTGTTGTTTTTTATTTTCTCT	9	36	1
GTCGCTTTTTAGGCGTATTTTCTTTATACTT	11	75	1
TAAGAAAAACGGGCGGATTATAGCCGTTTTT	12	25	1
AATAAGAAAAGTGCGGTTATTATAGGGGTTG	12	137	0
ATAGGAAATTTTGCTGTTTTTGCCTGCATTC	13	55	0
GATAATTTCGTGGCGGTTTTTTATGGCAAGT	13	163	1
TCAATAAAAAGTGCGGTTAATTTTAACCGCA	16	16	1
AGCAACAAGTGCGGTGATTTTAATAAAGGTT	20	46	1
          GTGCGGTTGATTTTTCACAAA	22	0	1
        GCTTGTGGTCTTTCTTTATAAAT	23	2	1
TGAAGTCTTGGCGTTATTTTTGTGTGAAATT	23	71	1
ACGGGATCCGTTGTTAATTTTGTAAAAAGTG	23	113	1
          * *********
MAP Score: 7.97771