AlignACE 3.0 10/20/99
AlignACE2 -i MJ/MJ_operons048_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241788
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MJ0397	300	DNA-directed RNA polymerase, subunit E' (rpoE1)

Motif 1
ATAATTAATGTAATTATTAATTTTGCCACAAAC	0	194	0
TTACATTAATTATTTATTGTTTTTTATAATCTC	0	214	1
ATATGACGATTAGTTACTCTTTTTTTATTAAAT	0	251	1
AATTTTCTCATATATATACTTTTCGTTTCATAA	0	124	1
TGGTTAATTATAAATATAGGTTTGTGGCAAAAT	0	175	1
CATACAAAAATTGTTATAAGTTATGAAACGAAA	0	144	0
          ** *****  ***
MAP Score: 4.10465

Motif 2
CAAACCTATATTTATAATTAACCATACAAA	0	169	0
TGTGGCAAAATTAATAATTACATTAATTAT	0	197	1
TAAAAAACAATAAATAATTAATGTAATTAT	0	210	0
TTTATTGTTTTTTATAATCTCACTAATATG	0	226	1
          **********
MAP Score: 2.24629

Motif 3
   ATTGGCGGACCCGAGGGGATTTGAACC	0	7	1
TTGAACCCCCGACCCCCGGCTTAGAAGGCC	0	30	1
AGATAAAGAGGACCCGTAGCCTAGCCTGGA	0	69	0
          **********
MAP Score: 1.8124