AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236325
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI1170_HI1171	41	HI1170: H. influenzae predicted coding region HI1170, HI1171: anthranilate synthase component II (trpG)
#1	HI1387	105	anthranilate synthase component I (trpE)
#2	HI1388.1	48	H. influenzae predicted coding region HI1388.1
#3	HI1389	52	anthanilate phosphoribosyltransferase (trpD)
#4	HI1389.1	36	indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase (trpC)

Motif 1
TTTTTAATCAAAAAGTATAAAAAATAAAAAT	1	19	1
AAACTAGTGCAAAAGGAATAAGTCAAGCCTG	1	50	0
GCACTAGTTTAATAGTACAAAATTTTCCAAA	1	71	1
AAAATTTTCCAAAAGGATAAATAAAT     	1	89	1
AACCGCACTTTAAAGGAGAAAAA        	2	35	1
        TAAAATATAGAAAATTAACAAAT	3	2	1
AAATCCATATACAAAGAAAAACAGGAATAGA	3	29	1
TATACGCCACAATAAGAAGAAAA        	4	23	1
          ******* ***
MAP Score: 12.4053

Motif 2
CTTTTTGATTAAAAATTGTATTTT      	1	4	0
ATTTTTAATCAAAAAGTATAAAAAATAAAA	1	18	1
AAAAAGTATAAAAAATAAAAATCAGGCTTG	1	28	1
CCTTTTGCACTAGTTTAATAGTACAAAATT	1	65	1
TCCTTTTGGAAAATTTTGTACTATTAAACT	1	76	0
AAAAGTGCGGTAATTTTTAACCGCACTTTA	2	17	1
        TAAAATATAGAAAATTAACAAA	3	2	1
   TAAAAGCTAATTTTATACGCCACAATA	4	7	1
          **********
MAP Score: 0.678736