AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions006_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254951
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PHS026	300	96aa long hypothetical protein
#1	PH0830	125	319aa long hypothetical protein
#2	PH0840	300	117aa long hypothetical protein
#3	PH0841	47	323aa long hypothetical protein
#4	PH1263	258	320aa long hypothetical protein

Motif 1
ATGTAGGATGGGAGGCCCTAAAAGTTCTTCAAGA	0	56	1
GGCCTCGTAGGAAGAAACGTGGAGAAAAGGAAAG	0	141	1
TAGGATTTGGGGAATCCCTTGGAGGCCGCTAGAA	0	200	1
CAGGGAAGCTGAGGTCTCTTGAAGATTTTAAAAT	2	52	1
TGAATGTAAAGAAGAACCTTGAAGATGTGGGGAG	2	117	1
TTGGGAAATTGAGCATCCAAAAAGCCTTAAATAC	2	271	1
TTGCAGAAGAGAGATTCCCTGAAGTTAAGTACTC	4	59	1
AAGTACTCCAGAGAGGACTGGGAGGGGACGTTGC	4	85	1
CCTAATTAAGGAAGATCCAAGGATACTTTCAATT	4	162	1
   GCTAACTGAAGATCCTAGGAGGATTAGCTTA	4	237	0
          ****  **  ****
MAP Score: 14.7915

Motif 2
TACTATCCCACACTCTTTCACTTAATATTT	0	15	0
GGCCTTAGATTAATTTTTCCACTAAAATTA	0	115	0
CCTCTTTCCTGACTCTTTCCTTTTCTCCAC	0	159	0
CACTAAGTAACCCTCTTTCCTGACTCTTTC	0	170	0
AATCTTTTAGTACTCTTTCCAG        	1	2	0
TTAAGCTTTTCACATTTTAAAATCTTCAAG	2	69	0
GGAGACTCCCCACATCTTCAAGGTTCTTCT	2	126	0
GTAAACATTATCCATTTTCATCGTGGAACC	2	166	0
ATAATGTTTACACTTTTTACTCAAAAGTAC	2	185	1
TAGGCAGAACGACTCATTCACTAAACTTTC	2	219	1
ACTCATTCACTAAACTTTCATCAATTCACC	2	230	1
CGTGATCCCAGACTCTTTGAAGGGCAC   	3	7	0
CTCTCTTCTGCAATTCTTCAGAAGTGTCTC	4	42	0
CAATTATGATTATTCTTTCCCTTAACGCAT	4	119	0
AGGATACTTTCAATTTTTCAAAGGAGCGTT	4	181	1
          **********
MAP Score: 10.4404

Motif 3
CAGCAAAATATTAAGTGAAAGAGTGTGGGATAGT	0	10	1
CTTCAAGAGGTTGAGGAGAAGAATAAAAAAAGTT	0	82	1
AAAAGTTAATTTTAGTGGAAAAATTAATCTAAGG	0	109	1
AAGAGGGTTACTTAGTGTAGGATTTGGGGAATCC	0	183	1
TTGATGAAAGTTTAGTGAATGAGTCGTTCTGCCT	2	220	0
GTTGCATGCGTTAAGGGAAAGAATAATCATAATT	4	114	1
GGAGGATTAGCTTAGTGTTTGAGTTTGACAAGTC	4	217	0
          ** **** * ** *
MAP Score: 8.62014

Motif 4
CCACGTTTCTTCCTACGAGGCCTTAGATTAA	0	132	0
TTTGGGGAATCCCTTGGAGGCCGCTAGAAAC	0	205	1
AAGCTGAGGTCTCTTGAAGATTTTAAAATGT	2	57	1
GTAAAGAAGAACCTTGAAGATGTGGGGAGTC	2	122	1
GAGTCTCCGTTTCCTGAAGGTTCCACGATGA	2	148	1
GAAGAGAGATTCCCTGAAGTTAAGTACTCCA	4	64	1
ATTGAAAGTATCCTTGGATCTTCCTTAATTA	4	164	0
AAGCTAATCCTCCTAGGATCTTCAGTTAGC 	4	238	1
          ********* *
MAP Score: 1.16122