AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions013_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255078
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH1363	211	493aa long hypothetical protein
#1	PH1748	271	192aa long hypothetical protein
#2	PH1749	50	482aa long hypothetical D-nopaline dehydrogenase
#3	PH1751	259	377aa long hypothetical sarcosine oxidase

Motif 1
TTTATTGTGGGCCGGCAACAGAGACCCAGC	1	210	0
CGGTGCATCCGCCCGCGGGATTAATGACCG	1	181	1
GTCAACCCGCCCCCGCAAGGTTTCGGGGTC	1	115	1
ATCATCATCCGCCCACAAGAATTTTAAGCT	1	28	1
AATTTTAATCGCCGACAGCGAGGGTACAAT	1	68	1
GTTAAAGAAGGCCGGAAGCAATTGCAAAAT	0	114	0
CTCACGCCGAGCCTACAGGGCCGGTGCATC	1	160	1
CCGGAAAGAAGCCGGAAGAAATTAGTTTGC	3	175	1
TTCAATCTTAGCCAGAAAGACCGGAAAGAA	3	155	1
GGTACAATACCCTCGCAAGGGCTCGGTCAA	1	90	1
AAAGAGCCAAGCTGAAAACGTCTTTGATTT	0	88	1
          **********
MAP Score: 11.2651

Motif 2
GGTTAAAGAAGGCCGGAAGCAATTGCAAAA	0	115	0
ACCGGAAAGAAGCCGGAAGAAATTAGTTTG	3	174	1
TTAATCCCGCGGGCGGATGCACCGGCCCTG	1	175	0
AAATTCTTGTGGGCGGATGATGATCCTTGC	1	22	0
ATCCTTGCCCAGCCTGAGGA          	1	0	0
CTTAATTAATAGATGGAGGCTAATCT    	1	255	1
GCTTTCATTGAGGAGGAAGATGAAAA    	3	243	1
AGGCCTGTTAGGATTGAAGCTTTCATTGAG	3	225	1
GCCCATTCCAATCCTGAGGAGTCTTCTCAA	3	90	0
CAAGGTTTCGGGGTCGATGAGCGGGGTGTG	1	130	1
          **********
MAP Score: 9.83111

Motif 3
TGGCTCTTTGCCCTTGCAACCTTTATTTTCT	0	66	0
   TCCTCAGGCTGGGCAAGGATCATCATCC	1	7	1
GGGTACAATACCCTCGCAAGGGCTCGGTCAA	1	89	1
CTCGCAAGGGCTCGGTCAACCCGCCCCCGCA	1	101	1
GGTCAACCCGCCCCCGCAAGGTTTCGGGGTC	1	114	1
GTGAGCACACCCCGCTCATCGACCCCGAAAC	1	134	0
TGGAATGGGCCCTTGTCAAGGTAGAACTTGC	3	110	1
TTTTCATCTTCCTCCTCAATGAAAGCTTCAA	3	238	0
          *** *******
MAP Score: 7.18746

Motif 4
AATAAAGGTTGCAAGGGCAAAGAGCCAAGCTGAAAACGTCT	0	70	1
CCTCAGGCTGGGCAAGGATCATCATCCGCCCACAAGAATTT	1	11	1
ATCGCCGACAGCGAGGGTACAATACCCTCGCAAGGGCTCGG	1	75	1
CCCTCGCAAGGGCTCGGTCAACCCGCCCCCGCAAGGTTTCG	1	99	1
CGGCCCTGTAGGCTCGGCGTGAGCACACCCCGCTCATCGAC	1	142	0
CGAGCCTACAGGGCCGGTGCATCCGCCCGCGGGATTAATGA	1	167	1
ATTAATGACCGCTGGGTCTCTGTTGCCGGCCCACAATAAAG	1	200	1
CCTCAGGATTGGAATGGGCCCTTGTCAAGGTAGAACTTGCA	3	101	1
          **   **  *     ** ***
MAP Score: 6.08507

Motif 5
AGAAAATAAAGGTTGCAAGGGCAAAGAGCCAAGCTGAAAACGT	0	66	1
TTTAATCGCCGACAGCGAGGGTACAATACCCTCGCAAGGGCTC	1	71	1
GGTACAATACCCTCGCAAGGGCTCGGTCAACCCGCCCCCGCAA	1	90	1
GCCCTGTAGGCTCGGCGTGAGCACACCCCGCTCATCGACCCCG	1	138	0
TCCCGCGGGCGGATGCACCGGCCCTGTAGGCTCGGCGTGAGCA	1	158	0
CGGGATTAATGACCGCTGGGTCTCTGTTGCCGGCCCACAATAA	1	196	1
CAAGTTCTACCTTGACAAGGGCCCATTCCAATCCTGAGGAGTC	3	97	0
          *   **  **** *      * *
MAP Score: 4.81316

Motif 6
GAAGGCCGGAAGCAATTGCAAAATCAAAGAC	0	107	0
GGGTTGACCGAGCCCTTGCGAGGGTATTGTA	1	92	0
ACTGATCTAGAGGAATTGAGAAGACTCCTCA	3	75	1
TTGTCAAGGTAGAACTTGCATACCTATAGTA	3	122	1
TAACCCTAGAGGAAATTGAAAAGCTCATAGA	3	34	1
CTTGGCTCTTTGCCCTTGCAACCTTTATTTT	0	68	0
GCATACCTATAGTAATTTCAATCTTAGCCAG	3	139	1
    CCCTCCAAAAATTGAAACAAATTCAAC	0	194	0
TATAGGTTAGGGAAAATGAAATTTGAAAATT	2	24	0
          ** ********
MAP Score: 3.75952

Motif 7
AGAAAATAAAGGTTGCAAGGGCAAAGAGCCAA	0	66	1
ATCATCATCCGCCCACAAGAATTTTAAGCTAT	1	28	1
TTTAATCGCCGACAGCGAGGGTACAATACCCT	1	71	1
GGTACAATACCCTCGCAAGGGCTCGGTCAACC	1	90	1
GTCAACCCGCCCCCGCAAGGTTTCGGGGTCGA	1	115	1
CTCACGCCGAGCCTACAGGGCCGGTGCATCCG	1	160	1
CGGTGCATCCGCCCGCGGGATTAATGACCGCT	1	181	1
CGGGATTAATGACCGCTGGGTCTCTGTTGCCG	1	196	1
          * ******** *
MAP Score: 3.57476

Motif 8
CCTCAGGCTGGGCAAGGATCATCATCCGCCCACAAGAAT	1	11	1
ATCGCCGACAGCGAGGGTACAATACCCTCGCAAGGGCTC	1	75	1
ACCCTCGCAAGGGCTCGGTCAACCCGCCCCCGCAAGGTT	1	98	1
TGTAGGCTCGGCGTGAGCACACCCCGCTCATCGACCCCG	1	138	0
CGAGCCTACAGGGCCGGTGCATCCGCCCGCGGGATTAAT	1	167	1
CTGATCTAGAGGAATTGAGAAGACTCCTCAGGATTGGAA	3	76	1
          ***   *  **  * ** *
MAP Score: 3.24169

Motif 9
          TCCTCAGGCTGGGCAAGGATCATCA	1	0	1
ATTTTAATCGCCGACAGCGAGGGTACAATACCCTC	1	69	1
ATGCACCGGCCCTGTAGGCTCGGCGTGAGCACACC	1	154	0
TCACGCCGAGCCTACAGGGCCGGTGCATCCGCCCG	1	161	1
TTGAGAAGACTCCTCAGGATTGGAATGGGCCCTTG	3	90	1
GCTAGATTTCCGATCAGGCCTGTTAGGATTGAAGC	3	210	1
          **  *****  ** *
MAP Score: 1.72953