AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions017_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248786
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB0066	95	PAB0066
#1	rfcS	27	PAB0068
#2	PAB0422	300	hypothetical protein
#3	rpoH	241	PAB7151

Motif 1
TTCTCGGTGCCCCGGTAGCCTAGCCTGGTGGGGCGGGGGAC	2	40	1
ATCCCCAGGTCGCGGGTTCAAATCCCGCCCGGGGCTCCAAG	2	86	1
ACCCGGGTCACGGGCTCCCAAAGCCCGCAGGATAGACCAAG	2	143	0
GAGCCCGTGACCCGGGTTCAAATCCCGGCGGCCCCACCAGA	2	167	1
CGGCTAATGCCCCGGTGGCTCAGCCTGGTAGAGCGGCCGCT	3	52	1
AGCGGCAGGTCCCGGGTTCAAAGCCCGGCCGGGGCTCCATT	3	98	1
          * ***   *  * ** *   *
MAP Score: 23.8756

Motif 2
ATTTCTCGGTGCCCCGGTAGCCTAGCCTGGTGGGGCG	2	38	1
GCGGGATTTGAACCCGCGACCTGGGGATTACAAGTCC	2	77	0
GCGGGTTCAAATCCCGCCCGGGGCTCCAAGAGGGGCC	2	97	1
GCCGTAGGGTAGCTTGGTCTATCCTGCGGGCTTTGGG	2	131	1
CCGGGATTTGAACCCGGGTCACGGGCTCCCAAAGCCC	2	158	0
CCGGGTTCAAATCCCGGCGGCCCCACCAGACTTTTTT	2	178	1
CTCGGCTAATGCCCCGGTGGCTCAGCCTGGTAGAGCG	3	50	1
CCGGGCTTTGAACCCGGGACCTGCCGCTTACCAAGCG	3	89	0
CCGGGTTCAAAGCCCGGCCGGGGCTCCATTCTAATAA	3	109	1
TGAAAAGCTTAAGCCGGGAGTTGGTGAAGTTCATCCT	3	187	1
          * *****  *  *  **
MAP Score: 15.9714

Motif 3
CAAAACTTTTCCAGGTGATGGAGC        	0	81	1
TTTTCCATTTCTCGGTGCCCCGGTAGCCTAGC	2	32	1
GGTAGCCTAGCCTGGTGGGGCGGGGGACTTGT	2	53	1
CTTGTAATCCCCAGGTCGCGGGTTCAAATCCC	2	80	1
CCCTCTTGGAGCCCCGGGCGGGATTTGAACCC	2	99	0
GCCCGGGGCTCCAAGAGGGGCCGTAGGGTAGC	2	112	1
GTCACGGGCTCCCAAAGCCCGCAGGATAGACC	2	146	0
CTTTGGGAGCCCGTGACCCGGGTTCAAATCCC	2	161	1
GGGTTCAAATCCCGGCGGCCCCACCAGACTTT	2	180	1
CGGCTAATGCCCCGGTGGCTCAGCCTGGTAGA	3	52	1
CTGCCGCTTACCAAGCGGCCGCTCTACCAGGC	3	74	0
TTGGTAAGCGGCAGGTCCCGGGTTCAAAGCCC	3	92	1
CGGGTTCAAAGCCCGGCCGGGGCTCCATTCTA	3	110	1
ATGAACTTCACCAACTCCCGGCTTAAGCTTTT	3	189	0
          ** ** ******
MAP Score: 13.6647

Motif 4
AAGATTTCCGAAACCTTCATAATGATTTTGGCGG	0	33	0
AAGGTTTCGGAAATCTTAATAATTCCTATGCCAA	0	50	1
TTCCTATGCCAAAACTTTTCCAGGTGATGGAGC 	0	72	1
TATCTCGATCATAACTTATTAATGCAATCCACTT	2	220	1
TTATCATATTAAAACTTTTACCTGTTTGTAAAAG	2	251	0
ATCACTTGCGAAAGCTTTATTAGAATGGAGCCCC	3	128	0
AAACATAAGTAAAGCTTATATATGAAAAGCTTAA	3	165	1
TTATATATGAAAAGCTTAAGCCGGGAGTTGGTGA	3	180	1
TTCATCCTAAAAAACTTTTCGGGGGGCAATTCTC	3	216	1
          *** *** *  ***
MAP Score: 12.518

Motif 5
CTTTTCCATTTCTCGGTGCCCCGGTAGCCT	2	31	1
CGGTAGCCTAGCCTGGTGGGGCGGGGGACT	2	52	1
ACTTGTAATCCCCAGGTCGCGGGTTCAAAT	2	79	1
CTCTTGGAGCCCCGGGCGGGATTTGAACCC	2	99	0
GCTTGGTCTATCCTGCGGGCTTTGGGAGCC	2	142	1
CGGGTTCAAATCCCGGCGGCCCCACCAGAC	2	179	1
CTTCAACTTCTTCTGGTGGAAGCTC     	2	285	1
TCGGCTAATGCCCCGGTGGCTCAGCCTGGT	3	51	1
CGGGTTCAAAGCCCGGCCGGGGCTCCATTC	3	110	1
TAAAAAACTTTTCGGGGGGCAATTCTCC  	3	223	1
          **********
MAP Score: 11.7423

Motif 6
CAGGCTAGGCTACCGGGGCACCGAGAAATGGAAAA	2	32	0
CTAGCCTGGTGGGGCGGGGGACTTGTAATCCCCAG	2	59	1
TAATCCCCAGGTCGCGGGTTCAAATCCCGCCCGGG	2	84	1
TTCAAATCCCGCCCGGGGCTCCAAGAGGGGCCGTA	2	102	1
GGCTTTGGGAGCCCGTGACCCGGGTTCAAATCCCG	2	159	1
AAAAAAGTCTGGTGGGGCCGCCGGGATTTGAACCC	2	180	0
CTCGGCTAATGCCCCGGTGGCTCAGCCTGGTAGAG	3	50	1
TAAGCGGCAGGTCCCGGGTTCAAAGCCCGGCCGGG	3	96	1
TTCAAAGCCCGGCCGGGGCTCCATTCTAATAAAGC	3	114	1
CTAAAAAACTTTTCGGGGGGCAATTCTCC      	3	222	1
          * ******* *   *
MAP Score: 11.2926

Motif 7
ACTGCCTTTTCCATTTCTCGGTGCCCCGGTAGCCT	2	26	1
CCCCGCCCCACCAGGCTAGGCTACCGGGGCACCGA	2	43	0
CTGGTGGGGCGGGGGACTTGTAATCCCCAGGTCGC	2	64	1
CTTGTAATCCCCAGGTCGCGGGTTCAAATCCCGCC	2	80	1
GGGTTCAAATCCCGCCCGGGGCTCCAAGAGGGGCC	2	99	1
GGTCTATCCTGCGGGCTTTGGGAGCCCGTGACCCG	2	146	1
CTTTGGGAGCCCGTGACCCGGGTTCAAATCCCGGC	2	161	1
GCTAATGCCCCGGTGGCTCAGCCTGGTAGAGCGGC	3	54	1
TTGGTAAGCGGCAGGTCCCGGGTTCAAAGCCCGGC	3	92	1
GGGTTCAAAGCCCGGCCGGGGCTCCATTCTAATAA	3	111	1
          ** ** * ***  **
MAP Score: 7.37491

Motif 8
CTAGGCTACCGGGGCACCGAGAAATGGAAAAGGCAGT	2	26	0
CAAGTCCCCCGCCCCACCAGGCTAGGCTACCGGGGCA	2	47	0
GGGGGACTTGTAATCCCCAGGTCGCGGGTTCAAATCC	2	74	1
CCCTCTTGGAGCCCCGGGCGGGATTTGAACCCGCGAC	2	94	0
GTAGCTTGGTCTATCCTGCGGGCTTTGGGAGCCCGTG	2	139	1
AAAGTCTGGTGGGGCCGCCGGGATTTGAACCCGGGTC	2	175	0
AACTTCAACTTCTTCTGGTGGAAGCTC          	2	283	1
TCTCGGCTAATGCCCCGGTGGCTCAGCCTGGTAGAGC	3	49	1
GGCCGCTTGGTAAGCGGCAGGTCCCGGGTTCAAAGCC	3	86	1
TTAGAATGGAGCCCCGGCCGGGCTTTGAACCCGGGAC	3	106	0
TATATGAAAAGCTTAAGCCGGGAGTTGGTGAAGTTCA	3	183	1
CCTAAAAAACTTTTCGGGGGGCAATTCTCC       	3	221	1
          *   * ** ** * ***
MAP Score: 6.7286

Motif 9
CATTTCTCGGTGCCCCGGTAGCCTAGCCTGGTGGGGC	2	37	1
CCCGGTAGCCTAGCCTGGTGGGGCGGGGGACTTGTAA	2	50	1
GGGGGACTTGTAATCCCCAGGTCGCGGGTTCAAATCC	2	74	1
GGTCGCGGGTTCAAATCCCGCCCGGGGCTCCAAGAGG	2	93	1
TAGCTTGGTCTATCCTGCGGGCTTTGGGAGCCCGTGA	2	140	1
GCGGGCTTTGGGAGCCCGTGACCCGGGTTCAAATCCC	2	156	1
CAAAAAAGTCTGGTGGGGCCGCCGGGATTTGAACCCG	2	179	0
TCTCGGCTAATGCCCCGGTGGCTCAGCCTGGTAGAGC	3	49	1
GGCCGCTTGGTAAGCGGCAGGTCCCGGGTTCAAAGCC	3	86	1
TTAGAATGGAGCCCCGGCCGGGCTTTGAACCCGGGAC	3	106	0
CCTAAAAAACTTTTCGGGGGGCAATTCTCC       	3	221	1
          *   * ** ****  **
MAP Score: 0.269901