AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions003_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254917
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0378	56	318aa long hypothetical UDP-glucose 4-epimerase
#1	PH0379	133	385aa long hypothetical protein
#2	PH0412	99	110aa long hypothetical protein
#3	PH0413	47	356aa long hypothetical glucose-1-phosphate thymidylyltransferase
#4	PH1022	300	416aa long hypothetical sugar-phosphate nucleotydyl transferase
#5	PH1209	45	259aa long hypothetical protein

Motif 1
TAAGGTCTAGTGGGTTAAGGGATATCC   	0	39	1
GAGAAGTACAAGATTTGAGGGAACCAGT  	2	8	0
ACTTCTCTATTGATTTAAGGATAGTGGTTC	2	31	1
TCATAAAATGATATTTAAGGTTTTCGAGAA	2	58	0
GGGTCGAGGGTGAGTTGAAGATAAAAGAGT	4	72	0
CTACTGGGAGAGGGTCGAGGGTGAGTTGAA	4	83	0
GAGTTAATCAAGTTTTCAGGGGAAGAACCC	4	112	0
TGCAAAGTCCATTTTAAAGGAGTTAATCAA	4	131	0
CAGCACCGGAAGTGTAAAGGCGTCAATTGC	4	158	0
GGAGTACAGGAGATTTAAGACCAGCACCGG	4	179	0
TAAAGGGGAACGGTTTAAGGATAACATCAG	4	280	1
    GTTGAAAGATTAAAAGTTGCAAATTA	5	29	0
          **********
MAP Score: 10.815

Motif 2
         GGATATCCCTTAACCCACTAG	0	45	0
GAAAGACTGGGAAAACCTTCTAC       	1	120	1
CTCAAATCTTGTACTTCTCTATTGATTTAA	2	19	1
AGTGGTTCTCGAAAACCTTAAATATCATTT	2	53	1
         CGACCTCCTTATCTTAATTTC	4	1	1
AAGAATAAAAGAACTTCTTTGGCTTCATAC	4	44	1
ACTCACCCTCGACCCTCTCCCAGTAGGGTT	4	87	1
TCCCAGTAGGGTTCTTCCCCTGAAAACTTG	4	104	1
AAAACTTGATTAACTCCTTTAAAATGGACT	4	126	1
TAAATCTCCTGTACTCCTCCCTAAGTGACA	4	192	1
AGTGACATAAGTTATCCTTCTCATTATCCT	4	215	1
TATCCTTATTTAACTTCTTCTCTAACGGAT	4	239	1
CTAACGGATTGAAAACCTTATAAAGGGGAA	4	260	1
TCCTTAAACCGTTCCCCTTTATAAGGTTTT	4	271	0
     CTGATGTTATCCTTAAACCGTTCCC	4	285	0
          **********
MAP Score: 10.0662

Motif 3
AATTAGTCTGGGCATAATTATATAACTGTAAG	0	11	1
 AGTGTAGTCGCGATTATTATAACGGTGATTA	1	9	1
TATTATAACGGTGATTATTATAATGGCCATTA	1	24	1
GAAAGACTGGGAAAACCTTCTAC         	1	120	1
TTCGAGAACCACTATCCTTAAATCAATAGAGA	2	34	0
AGTGGTTCTCGAAAACCTTAAATATCATTTTA	2	53	1
         CGACCTCCTTATCTTAATTTCCC	4	1	1
AGTGACATAAGTTATCCTTCTCATTATCCTTA	4	215	1
TATCCTTCTCATTATCCTTATTTAACTTCTTC	4	227	1
CTAACGGATTGAAAACCTTATAAAGGGGAACG	4	260	1
     CTGATGTTATCCTTAAACCGTTCCCCT	4	283	0
          *  *********
MAP Score: 9.99797

Motif 4
ACCGTTATAATAATCGCGACTACACT          	1	0	0
GTGATTATTATAATGGCCATTATACTAAGGAAGGAT	1	34	1
TCCCAGTCTTTCTACGCCCATAGAGTAAGAGCAACC	1	96	0
        ACTGGTTCCCTCAAATCTTGTACTTCTC	2	2	1
TTAAGGATAGTGGTTCTCGAAAACCTTAAATATCAT	2	45	1
GATAAATTTTTATTTCACACTAGAGTATTAACG   	3	24	1
CTCCTTATCTTAATTTCCCCGATACTTTCCAAGAAT	4	14	1
TAAAAGAACTTCTTTGGCTTCATACTCTTTTATCTT	4	49	1
CCAGTAGGGTTCTTCCCCTGAAAACTTGATTAACTC	4	106	1
GACTTTGCAATTGACGCCTTTACACTTCCGGTGCTG	4	152	1
ACACTTCCGGTGCTGGTCTTAAATCTCCTGTACTCC	4	173	1
ACATAAGTTATCCTTCTCATTATCCTTATTTAACTT	4	219	1
          *  *****   * ***
MAP Score: 9.01267