AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions004_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236327
 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	HI1386	300	H. influenzae predicted coding region HI1386
#2	HI1387	105	anthranilate synthase component I (trpE)
#3	HI1388.1	48	H. influenzae predicted coding region HI1388.1
#4	HI1389	52	anthanilate phosphoribosyltransferase (trpD)
#5	HI1389.1	36	indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase (trpC)

Motif 1
TACTGATGAACCAACCAACCAACCAACCAA	1	136	1
AACCAACCAACCAACCAACCAACCAACCAA	1	148	1
AACCAACCAACCAACCAACCAACCAACCAA	1	160	1
AACCAACCAACCAACCAACCAACCAACCAA	1	172	1
AACCAACCAACCAACCAACCAACCAAAATA	1	184	1
          **********
MAP Score: 26.4606

Motif 2
ATCTATACTGATGAACCAACCAACCAACCA	1	131	1
GAACCAACCAACCAACCAACCAACCAACCA	1	143	1
CAACCAACCAACCAACCAACCAACCAACCA	1	155	1
CAACCAACCAACCAACCAACCAACCAACCA	1	167	1
CAACCAACCAACCAACCAACCAACCAACCA	1	179	1
CAACCAACCAACCAACCAAAATAATAAAAC	1	191	1
          **********
MAP Score: 23.5639

Motif 3
GTAATTATGCAATAGAAAATATTTTTGG    	1	6	0
ATGTTTTGATAAGATTAGAAATAAGATTACGA	1	41	0
TATAAAAATGAAAAGGATCTATACTGATGAAC	1	115	1
CCAACCAACCAAAATAATAAAACCGTTGCGGT	1	198	1
TGGCTATTAAAAGCGTACAAAATCAAACTTAT	1	265	1
TTTTTAATCAAAAAGTATAAAAAATAAAAATC	2	19	1
GCACTAGTTTAATAGTACAAAATTTTCCAAAA	2	71	1
AAAATTTTCCAAAAGGATAAATAAAT      	2	89	1
AACCGCACTTTAAAGGAGAAAAA         	3	35	1
TAAAATATAGAAAATTAACAAATCCATATACA	4	10	1
ATACGCCACAATAAGAAGAAAA          	5	24	1
          ***** * ****
MAP Score: 11.1397

Motif 4
CGAGATGTAATTATGCAATAGAAAATATTTTTGG    	1	6	0
AAAATATACTTAATATAAGGCAAAATATGTTTTGATAA	1	61	0
TTATAATACCTTGATTAACTCAAAATATACTTAATATA	1	82	0
AATCAAGGTATTATAAAAATGAAAAGGATCTATACTGA	1	104	1
TTTGTACGCTTTTAATAGCCAAAGATAATTCTGGACGA	1	248	0
TTTTTTATACTTTTTGATTAAAAATTGTATTTT     	2	5	0
AATCAAAAAGTATAAAAAATAAAAATCAGGCTTGACTT	2	24	1
TTTGTACTATTAAACTAGTGCAAAAGGAATAAGTCAAG	2	54	0
          TAAAATATAGAAAATTAACAAATCCATA	4	0	1
TTTCTTCTTATTGTGGCGTATAAAATTAGCTTTTA   	5	7	0
          ** *  *    ***** *
MAP Score: 3.07985

Motif 5
CGTTATAATCAGGTCATTTTACGCAAA   	0	24	1
TAATTACATCTCGTAATCTTATTTCTAATC	1	31	1
GTAATCTTATTTCTAATCTTATCAAAACAT	1	43	1
GTATAGATCCTTTTCATTTTTATAATACCT	1	109	0
CAAGCCTGATTTTTATTTTTTATACTTTTT	2	28	0
TCAAAAAGTGCGGTAATTTTTAACCGCACT	3	14	1
TATATGGATTTGTTAATTTTCTATATTTTA	4	10	0
      TAAAAGCTAATTTTATACGCCACA	5	4	1
          **********
MAP Score: 1.64946