AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions007_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254975
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0893	52	161aa long hypothetical protein
#1	PH1454	265	241aa long hypothetical protein
#2	PH1455	247	120aa long hypothetical protein
#3	PH1456	82	174aa long hypothetical phaE product
#4	PH1516	149	303aa long hypothetical dihydroorotate dehydrogenase
#5	PH1874	80	298aa long hypothetical protein

Motif 1
TCCTAATGATTATATCCGCAATACTTTCCGTTGAA	1	43	1
GGAGGGATTTGCTAGCTGCTACCGTGGGAATGGCC	1	79	1
ATGCAAATAGGCTGACCGCGGCCATTCCCACGGTA	1	98	0
GGGCCGCTCCTATGGCCGCTTCCGTCATTGCAACG	1	164	0
TAATGGCGAAGATGAAGACAGCACCGCTCAGGGCC	1	194	0
TCTTAATAGCGATAGCAACGCTACTTAGCATGTAC	2	31	1
CGGCAACTAGTCTATCTACGGTAGTGGGTCCCCTG	2	74	0
TAGTCGTCATTATATCCACGGCAACTAGTCTATCT	2	92	0
ACGTTGCATTGGTATATGCAGTACTATCCTTCGCC	2	184	1
CCTCTATCAGGATATCAGCCCTAGTTGGATGATAG	4	21	1
TATCTTATATGATACCAGCTATCATCCAACTAGGG	4	39	0
TACAGTTTAATATAAAAACCTTATTTGAAACTTTG	4	123	1
          **** * **  ** *
MAP Score: 7.59812

Motif 2
AGATATAATTGTTCTCCTAATGATTATATCCGCAATACTTTCCGTTG	1	29	1
GGATTTGCTAGCTGCTACCGTGGGAATGGCCGCGGTCAGCCTATTTG	1	83	1
TCAGGCCCCCGACGTTGCAATGACGGAAGCGGCCATAGGAGCGGCCC	1	152	1
AGCGGCCATAGGAGCGGCCCTGAGCGGTGCTGTCTTCATCTTCGCCA	1	179	1
ACCCACTACCGTAGATAGACTAGTTGCCGTGGATATAATGACGACTA	2	80	1
GACTATCACAGTGGGATTAATGGTTCTTTTAGCCCTATACTACAAGA	2	122	1
GATCTTCCTTGACGTTGCATTGGTATATGCAGTACTATCCTTCGCCG	2	173	1
TCCAACTAGGGCTGATATCCTGATAGAGGGAGATAAAATA       	4	3	0
          *  *    * ***     *  *   **
MAP Score: 5.52061

Motif 3
ATACTTTCCGTTGAATGGAGGGATTTGCTAG	1	63	1
ATCTTCGCCATTAAAAGGACGTACAGGTATG	1	216	1
CGTACAGGTATGAAAGCGAGGAGGAAGAGAA	1	235	1
TGCAAGGTACTTGGAGGGAGGCCT       	2	233	1
GTGAAATTTATTAAAAGGAAAAATCC     	3	66	1
TGATATCCTGATAGAGGGAGATAAAATA   	4	7	0
GTCAATTCTATTAAAGGGAGGCCTTATCTTA	4	67	0
          ***** *****
MAP Score: 4.83186

Motif 4
ATATCCGCAATACTTTCCGTTGAATGGAGGGATTTGC	1	54	1
GATTTGCTAGCTGCTACCGTGGGAATGGCCGCGGTCA	1	84	1
CTGCTTCAGGCCCCCGACGTTGCAATGACGGAAGCGG	1	147	1
AGACCCTGTACATGCTAAGTAGCGTTGCTATCGCTAT	2	36	0
TTCAGGGGACCCACTACCGTAGATAGACTAGTTGCCG	2	72	1
GTAGATAGACTAGTTGCCGTGGATATAATGACGACTA	2	90	1
ATAATGACGACTATCACAGTGGGATTAATGGTTCTTT	2	114	1
AGGATGATCTTCCTTGACGTTGCATTGGTATATGCAG	2	168	1
GCAGTACTATCCTTCGCCGGGGTTATAGCATTTGCAA	2	201	1
          *   * **** *  ***
MAP Score: 3.47437

Motif 5
GATTATATCCGCAATACTTTCCGTTGAATGGAGGGATTTGC	1	50	1
TTTGCTAGCTGCTACCGTGGGAATGGCCGCGGTCAGCCTAT	1	86	1
TATGGCCGCTTCCGTCATTGCAACGTCGGGGGCCTGAAGCA	1	148	0
AATGACGGAAGCGGCCATAGGAGCGGCCCTGAGCGGTGCTG	1	170	1
GCGGCCCTGAGCGGTGCTGTCTTCATCTTCGCCATTAAAAG	1	192	1
       CAACCAGGTTTCTCTTCCTCCTCGCTTTCATACC	1	241	0
TGTTTATTTAGTCTTAATAGCGATAGCAACGCTACTTAGCA	2	20	1
ACGCTACTTAGCATGTACAGGGTCTTCAGGGGACCCACTAC	2	48	1
TGTGATAGTCGTCATTATATCCACGGCAACTAGTCTATCTA	2	91	0
ATTGGTATATGCAGTACTATCCTTCGCCGGGGTTATAGCAT	2	191	1
          **     * **  * **  **
MAP Score: 1.44876