AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_fusions009_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243205
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH997	31	carbamoyl-phosphate synthase, large subunit 
#1	MTH1127	90	dihydroorotase
#2	MTH1413	42	aspartate carbamoyltransferase
#3	MTH1415	175	ATP-dependent RNA helicase, eIF-4A family 
#4	MTH1445	64	glycinamide ribonucleotide synthetase

Motif 1
CACCGTCCACTCCATCCAGAACTATCCTTA	1	36	0
 CCAGAACTATCCTTTGAAGGCTCAAGCAT	1	71	0
    CAGTACCCCTTCCAGATTTTCATATA	2	26	0
        CCTCCCTTAAATCTTTTAGACC	3	2	1
AGGTTCAGGTTCCTTTCAGTGCTGAAAATC	3	126	0
AATGACAGATTCCGTTCAAG          	4	0	0
ATGACATATTTCCTATAAAATATATACTTT	4	37	1
ATAAAATATATACTTTCAAATAA       	4	51	1
          **********
MAP Score: 3.13742

Motif 2
ATGAGAGGAATGGGGATAAA          	0	21	1
TATCTCGCGGGACAGATTAATATT      	1	4	0
AATCTGTCCCGCGAGATAAATAAGGATAGT	1	16	1
AATCTTTTAGACCGGTTGAACACGCATCAT	3	19	1
GGGGGTTTATTGGGGATGATGCGTGTTCAA	3	34	0
AGGAATAAATGGGGGTTTATTGGGGATGAT	3	44	0
AGATTAAAAGAAGGAATAAATGGGGGTTTA	3	55	0
TTTGAGGTTTAAGAGATTAAAAGAAGGAAT	3	68	0
TAAATTGATGACCAGATAAAAGACC     	3	160	1
          **********
MAP Score: 0.92392