AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions013_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255092
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH1361	274	537aa long hypothetical proline permease
#1	PH1363	211	493aa long hypothetical protein
#2	PH1748	271	192aa long hypothetical protein
#3	PH1749	50	482aa long hypothetical D-nopaline dehydrogenase
#4	PH1751	259	377aa long hypothetical sarcosine oxidase

Motif 1
GGAACTAGCAGCGTGGCCCAAGCTGCTCCACTAAAACCCATCT	0	118	0
AATAAAGGTTGCAAGGGCAAAGAGCCAAGCTGAAAACGTCTTT	1	70	1
AAATTCTTGTGGGCGGATGATGATCCTTGCCCAGCCTGAGGA 	2	9	0
CCGAGCCCTTGCGAGGGTATTGTACCCTCGCTGTCGGCGATTA	2	73	0
CCTCGCAAGGGCTCGGTCAACCCGCCCCCGCAAGGTTTCGGGG	2	100	1
GTCGATGAGCGGGGTGTGCTCACGCCGAGCCTACAGGGCCGGT	2	142	1
GAGCCTACAGGGCCGGTGCATCCGCCCGCGGGATTAATGACCG	2	168	1
ATTAATGACCGCTGGGTCTCTGTTGCCGGCCCACAATAAAGTT	2	200	1
AGACTCCTCAGGATTGGAATGGGCCCTTGTCAAGGTAGAACTT	4	96	1
          **  **     *  **  * * *
MAP Score: 12.4075

Motif 2
GGTTTTAGTGGAGCAGCTTGGGCCACGCTGCTAGTTC	0	123	1
GAGAAAATAAAGGTTGCAAGGGCAAAGAGCCAAGCTG	1	65	1
         TCCTCAGGCTGGGCAAGGATCATCATCC	2	1	1
TTTTAATCGCCGACAGCGAGGGTACAATACCCTCGCA	2	70	1
GGGTACAATACCCTCGCAAGGGCTCGGTCAACCCGCC	2	89	1
GGTCAACCCGCCCCCGCAAGGTTTCGGGGTCGATGAG	2	114	1
GGCCCTGTAGGCTCGGCGTGAGCACACCCCGCTCATC	2	145	0
ATCCCGCGGGCGGATGCACCGGCCCTGTAGGCTCGGC	2	165	0
CCGGTGCATCCGCCCGCGGGATTAATGACCGCTGGGT	2	180	1
GCGGGATTAATGACCGCTGGGTCTCTGTTGCCGGCCC	2	195	1
ATTAGTTTGCCAAATGCTAGATTTCCGATCAGGCCTG	4	195	1
          *  * **  **** * *
MAP Score: 8.94053

Motif 3
AAGAAGGGGATATTAAACTTTATTGTGGGCCGGCAACA	2	220	0
ATCTATGAGCTTTTCAATTTCCTCTAGGGTTACATCGT	4	28	0
ATAAATTATAGCTTAAAATTCTTGTGGGCGGATGATGA	2	29	0
TTCTGGCTAAGATTGAAATTACTATAGGTATGCAAGTT	4	134	0
ATGTTGAATTTGTTTCAATTTTTGGAGGG         	1	192	1
ACGTCTTTGATTTTGCAATTGCTTCCGGCCTTCTTTAA	1	105	1
ATATTTACATTTTGAAATTTATTGGAGGTGACTTAGAT	0	84	1
    AGATGTTGTTAAACTGCATAAGGAGCTCTTTAAA	1	6	1
CGCTGTCGGCGATTAAAATTAATAAATTATAGCTTAAA	2	50	0
GAAAATGAAATTTGAAAATTTTTTAATAAAAAGG    	3	6	0
          * ** ** **  *   **
MAP Score: 7.59156

Motif 4
ATACCCCCTAAATCTTTATATACTATAAGTC	0	51	1
CAAAACCCATAAACTATCATTACTACAAAAG	0	172	0
TTGCCCTTGCAACCTTTATTTTCTCACTCTT	1	59	0
GGCCTTCTTTAACCTTTTTTTGCTAACCTAA	1	131	1
CAAGAATTTTAAGCTATAATTTATTAATTTT	2	43	1
AGGGGATATTAAACTTTATTGTGGGCCGGCA	2	223	0
CATTTTCCCTAACCTATATTTAG        	3	37	1
CCTGATCGGAAATCTAGCATTTGGCAAACTA	4	197	0
GTTAGGATTGAAGCTTTCATTGAGGAGGAAG	4	231	1
          ** ********
MAP Score: 7.41673

Motif 5
GGATCATCATCCGCCCACAAGAATTTTAAGCTATAAT	2	26	1
CTCGGTCAACCCGCCCCCGCAAGGTTTCGGGGTCGAT	2	111	1
TCTCTGTTGCCGGCCCACAATAAAGTTTAATATCCCC	2	216	1
GCCGGTGCATCCGCCCGCGGGATTAATGACCGCTGGG	2	179	1
CAATTGCTTCCGGCCTTCTTTAACCTTTTTTTGCTAA	1	120	1
CCCATCTAAGTCACCTCCAATAAATTTCAAAATGTAA	0	88	0
AAGTTTAATATCCCCTTCTTAATTAATAGATGGAGGC	2	238	1
          ****** *   *   **
MAP Score: 6.70704

Motif 6
TTGGAGGTGACTTAGATGGGTTTTAGTGGAG	0	105	1
GACAAAATTACGGGGAAGGAGTACTATGTAG	0	204	1
GAAGAGCTTACCAAGGAGGGTAGAGC     	0	258	1
 TCCTCAGGCTGGGCAAGGATCATCATCCGC	2	9	1
TTAAAATTCTTGTGGGCGGATGATGATCCTT	2	24	0
TTAATCGCCGACAGCGAGGGTACAATACCCT	2	72	1
TGACCGAGCCCTTGCGAGGGTATTGTACCCT	2	88	0
CGAAACCTTGCGGGGGCGGGTTGACCGAGCC	2	109	0
CCGCAAGGTTTCGGGGTCGATGAGCGGGGTG	2	127	1
CGCCGAGCCTACAGGGCCGGTGCATCCGCCC	2	164	1
TCATTAATCCCGCGGGCGGATGCACCGGCCC	2	177	0
TCCGATCAGGCCTGTTAGGATTGAAGCTTTC	4	218	1
          ** ********
MAP Score: 2.50134

Motif 7
ACTAGCAGCGTGGCCCAAGCTGCTCCACTA	0	128	0
GGTTAAAGAAGGCCGGAAGCAATTGCAAAA	1	115	0
AAATTCTTGTGGGCGGATGATGATCCTTGC	2	22	0
CGGGTTGACCGAGCCCTTGCGAGGGTATTG	2	94	0
AACCTTGCGGGGGCGGGTTGACCGAGCCCT	2	107	0
CAAGGTTTCGGGGTCGATGAGCGGGGTGTG	2	130	1
CGAGCCTACAGGGCCGGTGCATCCGCCCGC	2	167	1
ACCTTGACAAGGGCCCATTCCAATCCTGAG	4	102	0
          **********
MAP Score: 2.37659

Motif 8
ACGTCTTTGATTTTGCAATTGCTTCCGGCC	1	105	1
AATATTTACATTTTGAAATTTATTGGAGGT	0	83	1
ATGTTGAATTTGTTTCAATTTTTGGAGGG 	1	192	1
CATCTATGAGCTTTTCAATTTCCTCTAGGG	4	37	0
TATTAAAAAATTTTCAAATTTCATTTTCCC	3	16	1
AACCTAATGTTTTATAAATTATGACTTTAC	1	155	1
TAAGCTATAATTTATTAATTTTAATCGCCG	2	52	1
CCTGAGGAGTCTTCTCAATTCCTCTAGATC	4	78	0
          **********
MAP Score: 1.37587

Motif 9
AGAAAATAAAGGTTGCAAGGGCAAAGAGCCAAGCTGAAAACGTC	1	66	1
  TCCTCAGGCTGGGCAAGGATCATCATCCGCCCACAAGAATTT	2	8	1
TTTAATCGCCGACAGCGAGGGTACAATACCCTCGCAAGGGCTCG	2	71	1
GAAACCTTGCGGGGGCGGGTTGACCGAGCCCTTGCGAGGGTATT	2	95	0
CCTGTAGGCTCGGCGTGAGCACACCCCGCTCATCGACCCCGAAA	2	135	0
GCCGAGCCTACAGGGCCGGTGCATCCGCCCGCGGGATTAATGAC	2	165	1
AAACTTTATTGTGGGCCGGCAACAGAGACCCAGCGGTCATTAAT	2	200	0
          * * ** **   *     **   *
MAP Score: 0.48746

Motif 10
   ATAGTTTTCACCCCCTAATTTATGATATTT	0	7	1
CATATAAATACCCCCTAAATCTTTATATACTAT	0	44	1
ATCTAAGTCACCTCCAATAAATTTCAAAATGTA	0	89	0
CATAGTACTCCTTCCCCGTAATTTTGTCCCAAA	0	199	0
          CCCTCCAAAAATTGAAACAAATT	1	198	0
GATCATCATCCGCCCACAAGAATTTTAAGCTAT	2	27	1
GGTCAACCCGCCCCCGCAAGGTTTCGGGGTCGA	2	114	1
CCGGTGCATCCGCCCGCGGGATTAATGACCGCT	2	180	1
AGTTTAATATCCCCTTCTTAATTAATAGATGGA	2	239	1
AATTGAGAAGACTCCTCAGGATTGGAATGGGCC	4	88	1
          ***** *  ****
MAP Score: 0.161475