AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons016_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256066
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0612	170	245aa long hypothetical cell division inhibitor MinD
#1	PH0698	216	160aa long hypothetical nucleoside-diphosphate kinase
#2	PH0699	34	625aa long hypothetical threonyl-tRNA synthetase
#3	PH0768	40	256aa long hypothetical SOJ protein
#4	PHS024	167	62aa long hypothetical protein
#5	PH0948	77	175aa long hypothetical protein
#6	PH0949	82	295aa long hypothetical MRP protein
#7	PH1006	74	480aa long hypothetical prolyl-tRNA synthetase
#8	PH1581	75	139aa long hypothetical protein
#9	PH1600	101	217aa long hypothetical cell division inhibitor
#10	PH1694	31	445aa long hypothetical signal recognition particle protein
#11	PH1806	164	252aa long hypothetical protein

Motif 1
TTGTGTTGCTAAAAATTTTTAAATTTTGACCG	4	26	1
TATCTCCTCAAAAACCTTTTAAGTTATTATCC	11	48	0
TATGAACTTAAAAAACTTTTAAATTTATACCG	4	56	0
AAAATAGCACAAAGGTTTTTAAACTAGATTAG	6	35	1
CAAACGAACAAAAATCTTATAATCAAATTATA	11	90	1
TAATATCACAAAAATAATTTAAGCCAAAAAAT	4	86	1
ATTTAAGCCAAAAAATATTTAACTAGATAAAC	4	102	1
ACCCTGAAGGAACAGTTTTTAAGACGTTCGTC	5	23	0
TTATCTGAAGAAAAGAATTAAAAAGT      	3	4	0
ATCGAAACGTTAAATTTTTAAATGAATTGAGA	0	21	0
          ****  ******
MAP Score: 13.3432

Motif 2
ATTAATTTGAGAAGGTGTTCAGACTGATTC	0	53	1
AAAGCAGAACCAAGGAGGTTTAAAC     	0	155	1
TCTTAGCGTTAGAGGTGGTCTTTATCTCCT	1	27	1
TGCCACCTATAAAGGAGGTAGTTCTGATAA	1	76	0
CGGCAAGAACAAAGGGAGTCTTTGAGGGTA	1	120	0
TTAGGTTAAGGAAGGTGGTAGG        	2	22	1
GAATTCCGCTGAAGGGTGTTGTAGGG    	4	151	1
AAAATAGCACAAAGGTTTTTAAACTAGATT	6	35	1
AGCCTACAATCTAGGTGGTTAC        	7	62	1
TTACATTTATAATGGTGGTATATA      	8	4	0
TTTAAAAATGAAAGGGATTACATTTATAAT	8	21	0
     CTGGAAAAGGAGGTACAGGTAAAAC	9	5	1
TAATAACTTAAAAGGTTTTTGAGGAGATAG	11	51	1
          **********
MAP Score: 9.39777

Motif 3
CGATATTAATTTGAGAAGGTGTTCAGACTGATT	0	49	1
TATCAAAGCAGAACCAAGGAGGTTTAAAC    	0	151	1
ATAATCTTAGCGTTAGAGGTGGTCTTTATCTCC	1	23	1
AAAGCATAAGTAAACCAGGAGATAAAGACCACC	1	40	0
CCTGTGCCACCTATAAAGGAGGTAGTTCTGATA	1	77	0
CCTTTATAGGTGGCACAGGGGATTACCCCTACC	1	91	1
TGTTTTAGGTTAAGGAAGGTGGTAGG       	2	18	1
AATCAGCCTACAATCTAGGTGGTTAC       	7	58	1
ATATATAAATCTTGTCAGGTGATGGTAAC    	8	56	1
         CTGGAAAAGGAGGTACAGGTAAAA	9	1	1
ACTTAAAAGGTTTTTGAGGAGATAGGCAATATT	11	56	1
          ***   *******
MAP Score: 5.95399

Motif 4
AGACTGATTCCAAAAGAAATAAATATTCAAGCTAC	0	73	1
CATCCGATTATCAAAGCAGAACCAAGGAGGTTTAA	0	143	1
TTCTGATAAAGAAAAGCATAAGTAAACCAGGAGAT	1	50	0
GTTATCTGAAGAAAAGAATTAAAAAGT        	3	2	0
AAATTTGCTCCAAAAGCAACAAAATAGCACAAAGG	6	15	1
GATTAAAACGGTAACGAAAGATTAAAATTAAAAGA	7	24	1
GCTCAATTCGGGAAAGAAGTAATAGTAATTGACGC	9	66	1
     GGGTCTTAAAGTAAGATTAACTTGAAGGTG	10	5	1
GTCTAAGCGAGTAAAGAAGGATAATAACTTAAAAG	11	30	1
GGCAATATTCCAAACGAACAAAAATCTTATAATCA	11	80	1
          * ******  *  **
MAP Score: 5.19121

Motif 5
ATCAAAGCAGAACCAAGGAGGTTTAAAC       	0	152	1
AAGCATAAGTAAACCAGGAGATAAAGACCACCTCT	1	37	0
CTTTATAGGTGGCACAGGGGATTACCCCTACCCTC	1	92	1
TTATTATGGAAGGTTAGGAACTTACTTAAACCTTC	1	173	1
TCTTCAGATAACTTTAGGTGATTAA          	3	25	1
CTCAAGCCTTAGAATAGGGAATTCCGCTGAAGGGT	4	133	1
TTTATTGTTGAGTTAAGGGTATAAAAACATACCCT	5	50	0
TTTTTAAACTAGATTAGGTATTATCCATCGGGTGA	6	50	1
ATCAGCCTACAATCTAGGTGGTTAC          	7	59	1
ATAGTTTAAAAATGAAAGGGATTACATTTATAATG	8	20	0
        CTGGAAAAGGAGGTACAGGTAAAACCA	9	2	1
GAACTTATCAGGGCTAGGGGCTGACAAAT      	11	145	1
          **   *** * ****
MAP Score: 5.18478

Motif 6
AGCTTGAATATTTATTTCTTTTGGAATCAG	0	76	0
GTCAGCGATGCAATAATCTTAGCGTTAGAG	1	11	1
TAGGAACTTACTTAAACCTTCAAGGGGAAG	1	187	1
      ACTTTTTAATTCTTTTCTTCAGAT	3	4	1
AATTGTGTTGCTAAAAATTTTTAAATTTTG	4	24	1
ATTATGAACTTAAAAAACTTTTAAATTTAT	4	60	0
     CCCTACAACACCCTTCAGCGGAATT	4	152	0
GACGAACGTCTTAAAAACTGTTCCTTCAGG	5	23	1
GGGTATGTTTTTATACCCTTAACTCAACAA	5	51	1
TAATCTAGTTTAAAAACCTTTGTGCTATTT	6	36	0
TTCGTTACCGTTTTAATCTTAGGTTCAAAC	7	12	0
ATTCTTTTAATTTTAATCTTTCGTTACCGT	7	31	0
AACTATAATATATAAATCTTGTCAGGTGAT	8	49	1
CCTTTTAAGTTATTATCCTTCTTTACTCGC	11	36	0
CCTATCTCCTCAAAAACCTTTTAAGTTATT	11	52	0
TCCAAACGAACAAAAATCTTATAATCAAAT	11	88	1
          **********
MAP Score: 1.95338