AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_fusions009_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243209
 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	MTH1418	107	conserved protein
#5	MTH1445	64	glycinamide ribonucleotide synthetase

Motif 1
GGAATATTAGATGAGAGGAATGGGGATAAA   	0	11	1
GAGATAAATAAGGATAGTTCTGGATGGAGTGGA	1	28	1
GAGCCTTCAAAGGATAGTTCTGG          	1	77	1
       CCCATGATAGCTATGGTATAACCATG	4	3	1
ATTAATAATAATGACAGATTCCGTTCAAG    	5	6	0
          **** ** * ***
MAP Score: 7.30729

Motif 2
 TTTATCCCCATTCCTCTCATCTAATATTC	0	12	0
GACACCGTCCACTCCATCCAGAACTATCCT	1	38	0
      CAGTACCCCTTCCAGATTTTCATA	2	28	0
TAAGGTTCAGGTTCCTTTCAGTGCTGAAAA	3	128	0
ATAATGACAGATTCCGTTCAAG        	5	2	0
          **********
MAP Score: 2.75933

Motif 3
TCAGAATGCTTGAGCCTTCAAAGGATAGTTCTGG      	1	66	1
TTCCAGATTTTCATATATAACCCTATAACTTCC       	2	3	0
ATATTTAAATTTTTCTCTAAAGTTATAATTCATGGTTATA	4	26	0
TATTGGGTTTTTATACTTTATCGTATAGTTATACTATCAT	4	63	1
GAATCTGTCATTATTATTAATGACATATTTCCTATAAAAT	5	18	1
          TTATTTGAAAGTATATATTTTATAGGAAAT	5	44	0
          * **   * *    *** **
MAP Score: 2.1605