AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_sum_all020_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235610
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0311	199	176aa long hypothetical protein
#1	PH0612	170	245aa long hypothetical cell division inhibitor MinD
#2	PH0768	40	256aa long hypothetical SOJ protein
#3	PHS024	167	62aa long hypothetical protein
#4	PH0948	77	175aa long hypothetical protein
#5	PH0949	82	295aa long hypothetical MRP protein
#6	PH1581	75	139aa long hypothetical protein
#7	PH1600	101	217aa long hypothetical cell division inhibitor
#8	PH1694	31	445aa long hypothetical signal recognition particle protein
#9	PH1806	164	252aa long hypothetical protein

Motif 1
TTGTGTTGCTAAAAATTTTTAAATTTTGACCG	3	26	1
TATCTCCTCAAAAACCTTTTAAGTTATTATCC	9	48	0
TATGAACTTAAAAAACTTTTAAATTTATACCG	3	56	0
ATTTAAGCCAAAAAATATTTAACTAGATAAAC	3	102	1
TAATATCACAAAAATAATTTAAGCCAAAAAAT	3	86	1
GATATGTTCCAAAAGGTTTAAATCTGGTTATT	0	152	1
AAAATAGCACAAAGGTTTTTAAACTAGATTAG	5	35	1
TTATCTGAAGAAAAGAATTAAAAAGT      	2	4	0
CAAACGAACAAAAATCTTATAATCAAATTATA	9	90	1
TCATTTTTGTAAAAAGTTTAATAGTCTAACTA	0	36	0
ACCCTGAAGGAACAGTTTTTAAGACGTTCGTC	4	23	0
ATCGAAACGTTAAATTTTTAAATGAATTGAGA	1	21	0
GACTGATTCCAAAAGAAATAAATATTCAAGCT	1	74	1
          ****  ******
MAP Score: 19.7529

Motif 2
AATAAGGATCATTTTTGTAAAAAGTTTAATAGTCTAACT	0	37	0
TGATCCTTATTTTACCCTAAATAATTTGATATATATTCA	0	65	1
GACCCATACCTGATTTTGAATAAATTTCTTGAAAATTCC	0	112	0
ATGGGTCAGATATGTTCCAAAAGGTTTAAATCTGGTTAT	0	144	1
   GTTCGCAACTATCTCAATTCATTTAAAAATTTAACG	1	7	1
AATATTTATTTCTTTTGGAATCAGTCTGAACACCTTCTC	1	61	0
TCACCAATTGTGTTGCTAAAAATTTTTAAATTTTGACCG	3	19	1
TTTGACCGGTATAAATTTAAAAGTTTTTTAAGTTCATAA	3	50	1
AAGTTCATAATATCACAAAAATAATTTAAGCCAAAAAAT	3	79	1
CTTGAGTTTATCTAGTTAAATATTTTTTGGCTTAAATTA	3	100	0
AAAGCAACAAAATAGCACAAAGGTTTTTAAACTAGATTA	5	27	1
TACCACCATTATAAATGTAATCCCTTTCATTTTTAAACT	6	14	1
AAAGAAGGATAATAACTTAAAAGGTTTTTGAGGAGATAG	9	42	1
AACTATTTGATTTTTCATATATAATTTGATTATAAGATT	9	102	0
AGCCCTGATAAGTTCTCCAAACTATTTGATTTTTCATAT	9	121	0
          * *  *  ***   *** *
MAP Score: 11.7721

Motif 3
AATAACCAGATTTAAACCTTTTGGAACATATCTGAC	0	148	0
ATTATAAGATTTTTGTTCGTTTGGAATATTGCCTAT	9	77	0
AGCTTGAATATTTATTTCTTTTGGAATCAGTCTGAA	1	70	0
TTGATATATATTCAGCCCATTCGGAATTTTCAAGAA	0	90	1
TTTGTGCTATTTTGTTGCTTTTGGAGCAAATTTGTG	5	12	0
TTAAATTATTTTTGTGATATTATGAACTTAAAAAAC	3	72	0
          ***    * ** ****
MAP Score: 5.15506

Motif 4
TTTAAACTACCCTTGGGGTTAAGGAAA    	0	182	1
CCTACAACACCCTTCAGCGGAATTCCCTATT	3	145	0
AAAAACTGTTCCTTCAGGGTATGTTTTTATA	4	35	1
TAGGTATTATCCATCGGGTGAAAAGCGA   	5	64	1
      GTTACCATCACCTGACAAGATTTAT	6	60	0
       TCACCTTCAAGTTAATCTTACTTT	8	17	0
          ****** ****
MAP Score: 2.41987