AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236786
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0063	247	poly(A) polymerase (pcnB)
#1	HI0265	82	dihydroneopterin aldolase, putative
#2	HI1336	111	dihydropteroate synthase (folP-1)
#3	HI1464	111	dihydropteroate synthase (folP-2)

Motif 1
AATTTTAACCGCACTTTTGTATTTTTCAAT	0	18	0
AAAATTAACCGCACTTTTTTGCATTTAAAA	0	42	1
AAAATCCACTTGCCTTTTTCTTTACAAGAA	0	79	1
AAGAGCCAAGTCATTTATTTCCAACAACAA	0	109	1
CAACCTCTTTTGATTTTTTTGTCTTCTTGC	0	180	0
TTTAGAATGAGCACTTGTTTTGGCAACCTC	0	203	0
TCTTCGGAAAGGCTTTATTTTTTCCTAATG	2	24	1
TTTTTCCTAATGATTTTGTTCTTGGATGTA	2	42	1
TTTTGTTCTTGGATGTATTTCGCTATAATC	2	55	1
ATTTTTAGAGTGATTTTGGTGGGCGATTAT	2	79	0
TCTTCGGAAAGGCTTTATTTTTTCCTAATG	3	24	1
TTTTTCCTAATGATTTTGTTCTTGGATGTA	3	42	1
TTTTGTTCTTGGATGTATTTCGCTATAATC	3	55	1
ATTTTTAGAGTGATTTTGGTGGGCGATTAT	3	79	0
          **********
MAP Score: 17.7766

Motif 2
   TTCATTCTATTGAAAAATACAAAAGTGCGGT	0	7	1
CACTTTTTTGCATTTAAAAATGCAGGAAAATCCA	0	53	1
TCTTTTCTTGTAAAGAAAAAGGCAAGTGGATTTT	0	79	0
TTTTTCTTTACAAGAAAAGAGCCAAGTCATTTAT	0	93	1
TTTTTTGTCTTCTTGCCAAACAAATTTTTGATAT	0	162	0
TTGGCAAGAAGACAAAAAAATCAAAAGAGGTTGC	0	177	1
   TTTGCACTCCAGCAAGAAAAACTGTTCGTTA	1	7	1
ATAAAGCCTTTCCGAAGAAAGGCTTTGATGAG  	2	8	0
ACAAAATCATTAGGAAAAAATAAAGCCTTTCCGA	2	27	0
GAAATACATCCAAGAACAAAATCATTAGGAAAAA	2	42	0
GGTGGGCGATTATAGCGAAATACATCCAAGAACA	2	58	0
CGCTATAATCGCCCACCAAAATCACTCTAAAAAT	2	75	1
ATAAAGCCTTTCCGAAGAAAGGCTTTGATGAG  	3	8	0
ACAAAATCATTAGGAAAAAATAAAGCCTTTCCGA	3	27	0
GAAATACATCCAAGAACAAAATCATTAGGAAAAA	3	42	0
GGTGGGCGATTATAGCGAAATACATCCAAGAACA	3	58	0
CGCTATAATCGCCCACCAAAATCACTCTAAAAAT	3	75	1
          **  ******  **
MAP Score: 15.9876

Motif 3
CTCTTTTCTTGTAAAGAAAAAGGCAAGTGG	0	84	0
ATTTATTTCCAACAACAAAACGGAGTAAAT	0	121	1
TTTGATATAAGTAAGAATAATTTACTCCGT	0	140	0
TTGGCAAGAAGACAAAAAAATCAAAAGAGG	0	177	1
AAAAGAGGTTGCCAAAACAAGTGCTCATTC	0	199	1
TTGCACTCCAGCAAGAAAAACTGTTCGTTA	1	11	1
AAATCATTAGGAAAAAATAAAGCCTTTCCG	2	28	0
TACATCCAAGAACAAAATCATTAGGAAAAA	2	42	0
ATAATCGCCCACCAAAATCACTCTAAAAAT	2	79	1
AAATCATTAGGAAAAAATAAAGCCTTTCCG	3	28	0
TACATCCAAGAACAAAATCATTAGGAAAAA	3	42	0
ATAATCGCCCACCAAAATCACTCTAAAAAT	3	79	1
          **********
MAP Score: 11.1832

Motif 4
   CTCATCAAAGCCTTTCTTCGGAAAGGCTTTATT	2	7	1
GGAAAAAATAAAGCCTTTCCGAAGAAAGGCTTTGAT	2	13	0
TTGTTCTTGGATGTATTTCGCTATAATCGCCCACCA	2	57	1
   CTCATCAAAGCCTTTCTTCGGAAAGGCTTTATT	3	7	1
GGAAAAAATAAAGCCTTTCCGAAGAAAGGCTTTGAT	3	13	0
CCAAGAACAAAATCATTAGGAAAAAATAAAGCCTTT	3	31	0
TTGTTCTTGGATGTATTTCGCTATAATCGCCCACCA	3	57	1
          * *******     **
MAP Score: 10.5442

Motif 5
TTACTTATATCAAAAATTTGTTTGGCAAGAAGAC	0	156	1
        CTCATCAAAGCCTTTCTTCGGAAAGG	2	2	1
CATTAGGAAAAAATAAAGCCTTTCCGAAGAAAGG	2	20	0
TGATTTTGTTCTTGGATGTATTTCGCTATAATCG	2	52	1
        CTCATCAAAGCCTTTCTTCGGAAAGG	3	2	1
CATTAGGAAAAAATAAAGCCTTTCCGAAGAAAGG	3	20	0
TGATTTTGTTCTTGGATGTATTTCGCTATAATCG	3	52	1
          **  ** ** ****
MAP Score: 6.81286

Motif 6
TAACCGCACTTTTGTATTTTTCAATAGAAT	0	13	0
AACCGCACTTTTTTGCATTTAAAAATGCAG	0	48	1
TCCACTTGCCTTTTTCTTTACAAGAAAAGA	0	83	1
AAATAAATGACTTGGCTCTTTTCTTGTAAA	0	99	0
ATTTACTCCGTTTTGTTGTTGGAAATAAAT	0	121	0
CCAAACAAATTTTTGATATAAGTAAGAATA	0	151	0
TGGCAACCTCTTTTGATTTTTTTGTCTTCT	0	183	0
AAGAAAAACTGTTCGTTATTCTACCCAAAA	1	23	1
AAAGGCTTTATTTTTTCCTAATGATTTTGT	2	31	1
TTCCTAATGATTTTGTTCTTGGATGTATTT	2	45	1
CTTGGATGTATTTCGCTATAATCGCCCACC	2	62	1
AAAGGCTTTATTTTTTCCTAATGATTTTGT	3	31	1
TTCCTAATGATTTTGTTCTTGGATGTATTT	3	45	1
CTTGGATGTATTTCGCTATAATCGCCCACC	3	62	1
          **********
MAP Score: 5.40485

Motif 7
TCTTCGGAAAGGCTTTATTTTTTCCTAATGA	2	24	1
TTTTGTTCTTGGATGTATTTCGCTATAATCG	2	55	1
TCTTCGGAAAGGCTTTATTTTTTCCTAATGA	3	24	1
TTTTGTTCTTGGATGTATTTCGCTATAATCG	3	55	1
          ** ********
MAP Score: 5.26598