AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236571
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0837	53	response regulator (cpxR)
#1	HI0839	116	conserved hypothetical protein
#2	HI0884	191	aerobic respiration control protein ARCA (arcA)
#3	HI1379	300	phosphate regulon transcriptional regulatory protein (phoB)
#4	HI1708	62	transcriptional regulatory protein (ygiX)
#5	HI1709	114	conserved hypothetical protein

Motif 1
TATTCTTATTGTAGTGTGGTGAAAATAAAAAG	0	11	0
TCTTGCTGAAAAAGTGCGGTTATAATTTGCGG	1	80	1
CACAAAAAGGAAAATCAGGTAAAAAATCACCG	2	86	1
TAACAATAAAAAAGTGCGGTGATTTTTTACCT	2	102	0
AAACNNGATTATACTGTGGTTATAGTAACTCA	3	39	1
TATTCGCGGTAAAATGGGGTAGTTATTTTGAG	3	194	1
TTAAAAAGTAAAAGTTTGGTGAGAATGTATTA	3	234	1
TTATGGCATAAAAGTGAAGTGAGAAATAATAC	3	260	0
TTTTGTTTATAAAGTGCGGTCAATTTTTT   	4	43	1
          ****** *** *
MAP Score: 17.8803

Motif 2
TTCTCTTATTAAAAAGTAAAAGTTTGGTGA	3	226	1
TTTAGATCACAAAAAGGAAAATCAGGTAAA	2	79	1
TAACTAACTTAAAAAGGAAACGTT      	5	100	1
AGTCTTTTCAAAAAAGTATAGTCCTCTTAA	5	13	1
TTTCAGCAAGAAAAAAGAAATTATTTAGGT	1	61	0
CATACGCCAAAATAAGTATAAGGATGGAAA	2	171	1
     AATGTTAAAAATAAAAAAAATTTGG	1	5	1
ATTTATGGCATAAAAGTGAAGTGAGAAATA	3	264	0
GAATAATTGGTAAAAGGAATCTCCA     	0	38	1
GAATTGAGTATAAAAATATAGATGCTCGAA	2	11	1
TGTGTATTAAAACAAATAAATCTTAATAAA	5	46	0
ACCACACTACAATAAGAATAATTGGTAAAA	0	23	1
TTTACTTTTTAATAAGAGAACTCAAAATAA	3	216	0
          **********
MAP Score: 12.792