AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254908
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0379	133	385aa long hypothetical protein
#1	PH0412	99	110aa long hypothetical protein
#2	PH0413	47	356aa long hypothetical glucose-1-phosphate thymidylyltransferase
#3	PH1022	300	416aa long hypothetical sugar-phosphate nucleotydyl transferase
#4	PH1209	45	259aa long hypothetical protein

Motif 1
GTGATTATTATAATGGCCATTATACTAAGGAAGGATAGAGCTGGAG	0	34	1
TTCAAGACTTTCTCCAGCTCTATCCTTCCTTAGTATAATGGCCATT	0	45	0
        ACTGGTTCCCTCAAATCTTGTACTTCTCTATTGATTTA	1	2	1
TTAAGGATAGTGGTTCTCGAAAACCTTAAATATCATTTTATGAAAT	1	45	1
CTCCTTATCTTAATTTCCCCGATACTTTCCAAGAATAAAAGAACTT	3	14	1
TAAAAGAACTTCTTTGGCTTCATACTCTTTTATCTTCAACTCACCC	3	49	1
CCAGTAGGGTTCTTCCCCTGAAAACTTGATTAACTCCTTTAAAATG	3	106	1
ACACTTCCGGTGCTGGTCTTAAATCTCCTGTACTCCTCCCTAAGTG	3	173	1
ACATAAGTTATCCTTCTCATTATCCTTATTTAACTTCTTCTCTAAC	3	219	1
          ** *   *   ** **     *   *
MAP Score: 10.8907

Motif 2
GAAAGACTGGGAAAACCTTCTAC       	0	120	1
CTCAAATCTTGTACTTCTCTATTGATTTAA	1	19	1
AGTGGTTCTCGAAAACCTTAAATATCATTT	1	53	1
         CGACCTCCTTATCTTAATTTC	3	1	1
AAGAATAAAAGAACTTCTTTGGCTTCATAC	3	44	1
ACTCACCCTCGACCCTCTCCCAGTAGGGTT	3	87	1
AAAACTTGATTAACTCCTTTAAAATGGACT	3	126	1
TAAATCTCCTGTACTCCTCCCTAAGTGACA	3	192	1
AGTGACATAAGTTATCCTTCTCATTATCCT	3	215	1
TATCCTTATTTAACTTCTTCTCTAACGGAT	3	239	1
CTAACGGATTGAAAACCTTATAAAGGGGAA	3	260	1
TCCTTAAACCGTTCCCCTTTATAAGGTTTT	3	271	0
     CTGATGTTATCCTTAAACCGTTCCC	3	285	0
          **********
MAP Score: 10.8453

Motif 3
   AGTGTAGTCGCGATTATTATAACGGTGATTATTA	0	7	1
ATTATTATAATGGCCATTATACTAAGGAAGGATAGAG	0	37	1
AATTCAAGACTTTCTCCAGCTCTATCCTTCCTTAGTA	0	56	0
GAATTCGAGGTTGCTCTTACTCTATGGGCGTAGAAAG	0	88	1
TAGAAGGTTTTCCCAGTCTTTCTACGCCCATAGAGTA	0	105	0
ATCTTGTACTTCTCTATTGATTTAAGGATAGTGGTTC	1	24	1
CTTATCTTAATTTCCCCGATACTTTCCAAGAATAAAA	3	17	1
TTTGCAATTGACGCCTTTACACTTCCGGTGCTGGTCT	3	155	1
TGACATAAGTTATCCTTCTCATTATCCTTATTTAACT	3	217	1
TATCCTTATTTAACTTCTTCTCTAACGGATTGAAAAC	3	239	1
          *  *  *  ***** **
MAP Score: 2.61066

Motif 4
TAGAGCTGGAGAAAGTCTTGAATTCGAGGTTGCT	0	69	1
TATGGGCGTAGAAAGACTGGGAAAACCTTCTAC 	0	110	1
ACTGGTTCCCTCAAATCTTGTACTTCTCTATTGA	1	10	1
AGTGGTTCTCGAAAACCTTAAATATCATTTTATG	1	53	1
GTTCTTCCCCTGAAAACTTGATTAACTCCTTTAA	3	114	1
CTAACGGATTGAAAACCTTATAAAGGGGAACGGT	3	260	1
 GTTGAAAGATTAAAAGTTGCAAATTAAATTAGT	4	22	0
          * *** **** * *
MAP Score: 0.780968