AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions020_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248839
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
GCCTCAACCACCAGCATCATCAAACCCACAG	0	45	1
CATCAAACCCACAGGATCCTCCGCCAATGGT	0	62	1
CCTCCGACGCACTGCATCGTCATCGAGTCCA	0	144	1
CTAAAATTTTACAGAATTTTCAAGGTTGTAG	0	208	0
ATTAGTAGACAAAGGTTCATCGATAGAAAGA	1	32	1
AGTTCCTTGAAAAGGATACTCCAGCGATAGG	1	72	1
GAGACAACTTAAAGGAGCTCCAGAGGCTCCT	1	215	1
ATGAACTCAGCCAGGAGCCTCTGGAGCTCCT	1	227	0
          ******** **
MAP Score: 7.84276

Motif 2
TGAACTCAGCCAGGAGCCTCTGGAGCTCCT	1	227	0
AGACAACTTAAAGGAGCTCCAGAGGCTCCT	1	216	1
ATCAAACCCACAGGATCCTCCGCCAATGGT	0	63	1
GTTCCTTGAAAAGGATACTCCAGCGATAGG	1	73	1
CTTTTCTAATAAGGAGTCCTACAACCTTGA	0	190	1
AACACTTTGCAAGGATACCTTTTGAGGACA	1	266	1
TGAGGACATAGATGAGCTCCTA        	1	288	1
TATCCTTTTCAAGGAACTCTAGTTCCCTCT	1	60	0
          **********
MAP Score: 6.37089

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
CTCAACCACCAGCATCATCAAACCCACAGGA	0	47	1
CCTCCGCCAATGGTTCATTGGCCTTAGGGCC	0	79	1
TAGTAGACAAAGGTTCATCGATAGAAAGAGG	1	34	1
GAGGGAACTAGAGTTCCTTGAAAAGGATACT	1	61	1
CGATAGGGCTGAGTTCATTATAATCTATGGC	1	96	1
GGAGCCTCTGGAGCTCCTTTAAGTTGTCTCT	1	214	0
GCTCCTGGCTGAGTTCATTGGGGATAAACAC	1	240	1
       TAGGAGCTCATCTATGTCCTCAAA	1	286	0
          ********* *
MAP Score: 1.59084

Motif 5
CCTCAACCACCAGCATCATCAAACCCACAGGATCCT	0	46	1
ATCAAACCCACAGGATCCTCCGCCAATGGTTCATTG	0	63	1
GCCAATGGTTCATTGGCCTTAGGGCCGAACGGAAAC	0	84	1
GAAACGACCCCATCAGGTTCAAGTACAACCCTCCGA	0	115	1
CGACGCACTGCATCGTCATCGAGTCCAACCATTAAT	0	148	1
GGGCTGAGTTCATTATAATCTATGGCAGGAGGAGAA	1	101	1
TGAACTCAGCCAGGAGCCTCTGGAGCTCCTTTAAGT	1	221	0
          *** *** ** *   *
MAP Score: 0.849112