AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions013_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248723
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB1474	28	PAB1474
#1	PAB1471	28	PAB1471
#2	PAB1470	226	PAB1470

Motif 1
          TTTATTAATTATTTTGGGGTGGTGTGAT	0	0	1
          TTCTTCTTAACTTTTTGGAGGGATATCC	1	0	1
ACCTTGAGTTTATCTTCATCCATTTAGGCCCTATTATC	2	18	1
CCCTATTATCTTTATAAAAGACTTTCGGTGAAAGTATA	2	46	1
AAGCGTTACGACAATTGTCAAATTTTGGCATTACCTAT	2	111	0
TTTTTGAATTTGATTTATGTAGTTTTCGGTGCTAAGCT	2	151	0
TAATCCGAGTTCAATCTTGAATTTTTGAATTTGATTTA	2	172	0
TGAACTCGGATTAATTGAAAGCTTAAGGGGGCAGAAAA	2	197	1
          *   ** *  * *** **
MAP Score: 5.73694

Motif 2
      TTCTTCTTAACTTTTTGGAGGGATAT	1	4	1
 TACTCATCACCTTGAGTTTATCTTCATCCAT	2	9	1
CCATTTAGGCCCTATTATCTTTATAAAAGACT	2	37	1
TATACTTTCACCGAAAGTCTTTTATAAAGATA	2	52	0
TTGACAATTGTCGTAACGCTTTGAGCTTAGCA	2	128	1
CCGAGTTCAATCTTGAATTTTTGAATTTGATT	2	174	0
CTTTTCTGCCCCCTTAAGCTTTCAATTAATCC	2	204	0
          **** * *****
MAP Score: 4.72768