AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248780
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB0066	95	PAB0066
#1	rfcS	27	PAB0068
#2	rpoH	241	PAB7151

Motif 1
GCGGAATGTTATATTTAGGGAGGGCCT      	0	4	0
CCCTAAATATAACATTCCGCCAAAATCATTATG	0	17	1
AATCATTATGAAGGTTTCGGAAATCTTAATAAT	0	40	1
TCACCTGGAAAAGTTTTGGCATAGGAATTATTA	0	66	0
AAAGTATATAAAATTTTCGGTAAT         	2	1	0
ATTAGCCGAGAATTCCTCAGAGGTAGAAAGTAT	2	27	0
ATTCTCGGCTAATGCCCCGGTGGCTCAGCCTGG	2	47	1
TCCCGGGTTCAAAGCCCGGCCGGGGCTCCATTC	2	107	1
CATTCTAATAAAGCTTTCGCAAGTGATATAAAA	2	135	1
GAACTTCACCAACTCCCGGCTTAAGCTTTTCAT	2	186	0
CATCCTAAAAAACTTTTCGGGGGGCAATTCTCC	2	218	1
          **  ****** **
MAP Score: 9.0944

Motif 2
 CTAAAATTAGAGGCCTCTCGATAGGTA  	1	8	0
GGCTAATGCCCCGGTGGCTCAGCCTGGTAG	2	53	1
CGCTTACCAAGCGGCCGCTCTACCAGGCTG	2	72	0
CGCTTGGTAAGCGGCAGGTCCCGGGTTCAA	2	89	1
GAATGGAGCCCCGGCCGGGCTTTGAACCCG	2	110	0
          **********
MAP Score: 8.0133

Motif 3
GGCCGCTTGGTAAGCGGCAGGTCCCGGGTTCAA	2	86	1
TGCCGCTTACCAAGCGGCCGCTCTACCAGGCTG	2	72	0
ATGAAAAGCTTAAGCCGGGAGTTGGTGAAGTTC	2	186	1
CATAATGATTTTGGCGGAATGTTATATTTAGGG	0	17	0
GGTTCAAAGCCCGGCCGGGGCTCCATTCTAATA	2	112	1
CACCGGGGCATTAGCCGAGAATTCCTCAGAGGT	2	36	0
    CTAAAATTAGAGGCCTCTCGATAGGTA  	1	8	0
AAAAAACTTTTCGGGGGGCAATTCTCC      	2	224	1
AAAAGTTTTTTAGGATGAACTTCACCAACTCCC	2	202	0
GCCGCTCTACCAGGCTGAGCCACCGGGGCATTA	2	56	0
          * *******  **
MAP Score: 5.43707

Motif 4
TAATGATTTTGGCGGAATGTTATATTTAGG	0	18	0
  CTAAAATTAGAGGCCTCTCGATAGGTA 	1	9	0
CCGCTTACCAAGCGGCCGCTCTACCAGGCT	2	73	0
CCGCTTGGTAAGCGGCAGGTCCCGGGTTCA	2	88	1
TGGAGCCCCGGCCGGGCTTTGAACCCGGGA	2	107	0
AAAAGCTTAAGCCGGGAGTTGGTGAAGTTC	2	189	1
          **********
MAP Score: 4.13008

Motif 5
   TACCTATCGAGAGGCCTCTAATTTTAG  	1	7	1
TCAGCCTGGTAGAGCGGCCGCTTGGTAAGCGG	2	71	1
GCTTGGTAAGCGGCAGGTCCCGGGTTCAAAGC	2	90	1
AATGGAGCCCCGGCCGGGCTTTGAACCCGGGA	2	107	0
AAAAACTTTTCGGGGGGCAATTCTCC      	2	225	1
          **** **** **
MAP Score: 2.5261