AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions012_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248716
 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
  GGTGAATTCAAGGTGATGCCCTACCAAT	0	8	1
AAAGAGCATAAATGGTAAGCACAGGTCCCT	0	110	1
AGTTAAGCCGCAAGGAGAGAAAACCACTAT	0	157	1
CTAGGATCCTAAAGGAGCTGGGTCTAATAG	0	205	1
GAATATGGAACAAGGGAAGCTCCTAAACCC	0	234	1
GTAACCCTAACTAGGGAAGGCAAGTTCATT	0	264	1
CCTATTTTACCAAGGTGAACGCT       	1	30	1
TTCTACTCTCCAAGGTGCTCCAG       	2	31	1
          **********
MAP Score: 6.51677

Motif 3
GTGATGCCCTACCAATGGAAAATCCTGGAGT	0	22	1
GTTAAGCCGCAAGGAGAGAAAACCACTATCA	0	158	1
TAGAATATGGAACAAGGGAAGCTCCTAAACC	0	232	1
CCGTAACCCTAACTAGGGAAGGCAAGTTCAT	0	262	1
   AGCGTTCACCTTGGTAAAATAGGATTTT	1	25	0
GAGAGTAGAAAAAGAGAGAAGGTTAAAAACT	2	10	0
   TCAGACTAACCTGGCAAAACCCTCTAAA	3	7	1
          *** *******
MAP Score: 4.99107