AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions012_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248713
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	tkt1	300	PAB0295
#1	tmpC-like	43	PAB0302
#2	rbsA	44	PAB0303
#3	aroA	28	PAB0306

Motif 1
CCCTACCAATGGAAAATCCTGGAGTGAAAG	0	28	1
AGCACAGGTCCCTAAACGCTCTACTGGAAG	0	127	1
TCTCCTTGCGGCTTAACTCTTCCAGTAGAG	0	145	0
CAACATTAAAGCTCAACGCTAGGATCCTAA	0	187	1
AAGGGAAGCTCCTAAACCCGTAACCCTAAC	0	245	1
       CCTCCAGAATGCTGAGAATGAAC	0	287	0
TTATAAGTGACCAAAATCCTATTTTACCAA	1	13	1
ATTTTACCAAGGTGAACGCT          	1	33	1
GACTAACCTGGCAAAACCCTCTAAA     	3	13	1
          **********
MAP Score: 13.4855

Motif 2
TTGGTAGGGCATCACCTTGAATTCACC    	0	6	0
CTTTCACTCCAGGATTTTCCATTGGTAGGGC	0	27	0
CAGCTCCTTTAGGATCCTAGCGTTGAGCTTT	0	194	0
AGGATCCTAAAGGAGCTGGGTCTAATAGAAT	0	207	1
TTACGGGTTTAGGAGCTTCCCTTGTTCCATA	0	237	0
AATGCTGAGAATGAACTTGCCTTCCCTAGTT	0	272	0
GTTCATTCTCAGCATTCTGGAGG        	0	287	1
TTGGTAAAATAGGATTTTGGTCACTTATAAA	1	12	0
      AGCGTTCACCTTGGTAAAATAGGAT	1	28	0
      CTGGAGCACCTTGGAGAGTAGAAAA	2	29	0
     TTTAGAGGGTTTTGCCAGGTTAGTCT	3	12	0
          **** ******
MAP Score: 7.42873

Motif 3
CATTGGTAGGGCATCACCTTGAATTCACC 	0	9	0
CTCTTAAGAACTTTCACTCCAGGATTTTCC	0	38	0
AGCACAGGTCCCTAAACGCTCTACTGGAAG	0	127	1
TCTCCTTGCGGCTTAACTCTTCCAGTAGAG	0	145	0
CAACATTAAAGCTCAACGCTAGGATCCTAA	0	187	1
AAGGGAAGCTCCTAAACCCGTAACCCTAAC	0	245	1
        AGCGTTCACCTTGGTAAAATAG	1	31	0
 AGTTTTTAACCTTCTCTCTTTTTCTACTC	2	9	1
TCTCTCTTTTTCTACTCTCCAAGGTGCTCC	2	22	1
GACTAACCTGGCAAAACCCTCTAAA     	3	13	1
          **********
MAP Score: 1.5081