AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions007_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254969
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0893	52	161aa long hypothetical protein
#1	PH1454	265	241aa long hypothetical protein
#2	PH1516	149	303aa long hypothetical dihydroorotate dehydrogenase
#3	PH1874	80	298aa long hypothetical protein

Motif 1
TCCTAATGATTATATCCGCAATACTTTCCGTTGAA	1	43	1
GGAGGGATTTGCTAGCTGCTACCGTGGGAATGGCC	1	79	1
ATGCAAATAGGCTGACCGCGGCCATTCCCACGGTA	1	98	0
GGGCCGCTCCTATGGCCGCTTCCGTCATTGCAACG	1	164	0
TGGCGAAGATGAAGACAGCACCGCTCAGGGCCGCT	1	191	0
CCTCTATCAGGATATCAGCCCTAGTTGGATGATAG	2	21	1
TATCTTATATGATACCAGCTATCATCCAACTAGGG	2	39	0
TATCATATAAGATAAGGCCTCCCTTTAATAGAATT	2	60	1
          **** * **  ** *
MAP Score: 7.11107

Motif 2
ATAACTTTTGGTTTTAAATATGAAAATGTTTTTA	0	27	1
TATAGCATGTGTTGAAGATATAATTGTTCTCCTA	1	14	1
AAACAGTATCGATGCAAATAGGCTGACCGCGGCC	1	110	0
TATCCTGATAGAGGGAGATAAAATA         	2	1	0
ATGATAGCTGGTATCATATAAGATAAGGCCTCCC	2	49	1
TAGAATTACAGTTTAATATAAAAACCTTATTTGA	2	117	1
     TCAAAGTTTCAAATAAGGTTTTTATATTA	2	130	0
CCAACCAATAGTTTACAATAAGTTTATAAAAACA	3	25	1
          **** * *** * *
MAP Score: 6.01209

Motif 3
GAGGGATTTGCTAGCTGCTACCGTGGGAATGGCCGCGGTCAGC	1	80	1
TACCGTGGGAATGGCCGCGGTCAGCCTATTTGCATCGATACTG	1	98	1
TTTCCTGCTTCAGGCCCCCGACGTTGCAATGACGGAAGCGGCC	1	143	1
CGTTGCAATGACGGAAGCGGCCATAGGAGCGGCCCTGAGCGGT	1	164	1
GGAAGCGGCCATAGGAGCGGCCCTGAGCGGTGCTGTCTTCATC	1	176	1
AGCGGCCCTGAGCGGTGCTGTCTTCATCTTCGCCATTAAAAGG	1	191	1
TAGTTGGATGATAGCTGGTATCATATAAGATAAGGCCTCCCTT	2	42	1
          *  ** ** * * *       **
MAP Score: 3.07907

Motif 4
CATTTTCATATTTAAAACCAAAAGTTATGGACAAAATTGGGAAA	0	11	0
ATCACCTAATTTTAGAATTACAGTTTAATATAAAAACCTTATTT	2	105	1
AGAATTACAGTTTAATATAAAAACCTTATTTGAAACTTTGA   	2	118	1
CAACCAATAGTTTACAATAAGTTTATAAAAACAAAATGTTCAGA	3	26	1
TTACAATAAGTTTATAAAAACAAAATGTTCAGAACCTAGTGTAA	3	37	1
          **** **  *     *      **
MAP Score: 1.45999

Motif 5
ATTTCCCAATTTTGTCCATAACTTTTGGTTT	0	10	1
TCAGATCACCTAATTTTAGAATTACAGTTTA	2	101	1
        TCAAAGTTTCAAATAAGGTTTTT	2	136	0
TATCCAACCAATAGTTTACAATAAGTTTATA	3	22	1
TAGTTTACAATAAGTTTATAAAAACAAAATG	3	33	1
ATAAAAACAAAATGTTCAGAACCTAGTGTAA	3	50	1
AACCTAGTGTAATGTCCAAAA          	3	69	1
          ******** **
MAP Score: 0.654153