AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions020_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248849
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB1619	300	hypothetical protein
#1	PAB1412	300	hypothetical protein

Motif 1
CTGGAGTATCCTTTTCAAGGAACTCTAGTTC	1	65	0
TCATTATAATCTATGGCAGGAGGAGAATTGG	1	110	1
TATTACTTCACTTTGCTAGGAACAAGCCTCA	1	152	1
TTTAAGTTGTCTCTGTAAGGCTTTTCCGTTA	1	197	0
CCCCAATGAACTCAGCCAGGAGCCTCTGGAG	1	232	0
GGGATAAACACTTTGCAAGGATACCTTTTGA	1	260	1
TGCAAGGATACCTTTTGAGGACATAGATGAG	1	273	1
          ****** ****
MAP Score: 10.1301

Motif 2
GCTCCTGGCTGAGTTCATTGGGGATAAACA	1	240	1
GAGGGAACTAGAGTTCCTTGAAAAGGATAC	1	61	1
GGAGCCTCTGGAGCTCCTTTAAGTTGTCTC	1	215	0
TAGTAGACAAAGGTTCATCGATAGAAAGAG	1	34	1
       TAGGAGCTCATCTATGTCCTCAA	1	287	0
CGATAGGGCTGAGTTCATTATAATCTATGG	1	96	1
CCTCCGCCAATGGTTCATTGGCCTTAGGGC	0	79	1
GGAGCTCCAGAGGCTCCTGGCTGAGTTCAT	1	228	1
CAAGGTTGTAGGACTCCTTATTAGAAAAGT	0	189	0
CCATTGGCGGAGGATCCTGTGGGTTTGATG	0	62	0
GTCCTCAAAAGGTATCCTTGCAAAGTGTTT	1	265	0
          **********
MAP Score: 8.89918

Motif 3
TCATCAAACCCACAGGATCCTCCGCCAATGG	0	61	1
GATCCTCCGCCAATGGTTCATTGGCCTTAGG	0	76	1
ACTTTTCTAATAAGGAGTCCTACAACCTTGA	0	189	1
CATTAGTAGACAAAGGTTCATCGATAGAAAG	1	31	1
CATCGATAGAAAGAGGGAACTAGAGTTCCTT	1	49	1
GAGTTCCTTGAAAAGGATACTCCAGCGATAG	1	71	1
AAAAGCCTTACAGAGACAACTTAAAGGAGCT	1	203	1
AAAGGAGCTCCAGAGGCTCCTGGCTGAGTTC	1	225	1
AAACACTTTGCAAGGATACCTTTTGAGGACA	1	265	1
          ****** ****
MAP Score: 5.96714

Motif 4
CCAATGGTTCATTGGCCTTAGGGCCGAACG	0	85	1
TCGTTTGGATATTGGTGATACTAAAATTTT	0	229	0
TACTCCAGCGATAGGGCTGAGTTCATTATA	1	88	1
CAGGAGGAGAATTGGGAAGACCGAGTTATT	1	126	1
GGCTGAGTTCATTGGGGATAAACACTTTGC	1	246	1
          **********
MAP Score: 0.683801