AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions015_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236732
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0354	300	ABC transporter, ATP-binding protein
#1	HI0357	21	thiamine biosynthesis protein, putative
#2	HI0415	300	hydroxyethylthiazole kinase

Motif 1
ATTTAAAAATGCTTTTCTTGTTCCATTCGGATA	0	66	1
TATCATCTCAGCCTTTCGGCACCCCGACTAAAA	0	151	0
TCAGTGCTAACTGTTTCAGGTTCACGGGTATCA	0	179	0
GGATTTTTTGGCATATTAGTTTCCTACGTCAGT	0	207	0
GCCAAAAAATCCATTTTCTTTTCATTCCATTTC	0	228	1
TCTTTTCATTCCATTTCTTATCCTTTCTTTTTT	0	244	1
TATCATCTCAGCCTTTCGGCACCCCGACTAAAA	2	101	0
TCAGTGCTAACTGTTTCAGGTTCACGGGTATCA	2	129	0
TGAATATGTGGCATATTAGTTTCCTACGTCAGT	2	157	0
ACGATTTTATCCTGTTTATTTTCCCAATTTTCT	2	203	1
TGAATAGCGGGCATTTTTGTTTATTTTATATTC	2	267	1
          ** **** * ***
MAP Score: 14.5782

Motif 2
TCTACCAAACAAGCGTAAACTTACCAACAGTT	0	120	1
CTGAGATGATACCCGTGAACCTGAAACAGTTA	0	173	1
        TAAGCGGTCAAATTCTTCTCATTA	2	2	1
AGAAAAAACAAGCGGTCAAATTTTTCCCTCAT	2	42	0
TCTTGAAAAGAAGCGTAAACTTCTTTCGACTT	2	71	1
CTGAGATGATACCCGTGAACCTGAAACAGTTA	2	123	1
          * **** *****
MAP Score: 9.083

Motif 3
CTGAAACAGTTAGCACTGACGTAGGAAACTAATATGC	0	193	1
CTGAAACAGTTAGCACTGACGTAGGAAACTAATATGC	2	143	1
TTTCGGCACCCCGACTAAAAGTCGAAAGAAGTTTACG	2	84	0
CAACAGTTTTTAGTCGGGGTGCCGAAAGGCTGAGATG	0	144	1
GCTGAGATGATACCCGTGAACCTGAAACAGTTAGCAC	2	122	1
GCTGAGATGATACCCGTGAACCTGAAACAGTTAGCAC	0	172	1
       TGCTCGCCTCAATGATTAAAGGGAGTGCGT	0	280	0
TTGTTTTTTCTTGAAAAGAAGCGTAAACTTCTTTCGA	2	63	1
AGGTTTCTATCCGAATGGAACAAGAAAAGCATTTTTA	0	69	0
CTTCTCATTATTTGCAAAATGAGGGAAAAATTTGACC	2	24	1
        CTTTTCATTAAAGGAGAAAAA        	1	2	1
TTTAGTCGGGGTGCCGAAAGGCTGAGATGATACCCGT	2	102	1
TAAAGGGAGTGCGTAATAAAAAAGAAAGGATAAGAAA	0	257	0
          * * *  ** *  ****
MAP Score: 9.03002

Motif 4
CTTGTTTGGTAGAAAAAACAAGCAATTAGGT	0	102	0
CTTCTTTTCAAGAAAAAACAAGCGGTCAAAT	2	53	0
TGTTGAATATAAAATAAACAAAAATGCCCGC	2	273	0
GGAGTGCGTAATAAAAAAGAAAGGATAAGAA	0	258	0
GAAAATTGGGAAAATAAACAGGATAAAATCG	2	204	0
TAAGAAATGGAATGAAAAGAAAATGGATTTT	0	233	0
CGGCACCCCGACTAAAAACTGTTGGTAAGTT	0	137	0
          * *********
MAP Score: 4.93046

Motif 5
TATCTTAGCAAGAGAAATTTAAAAATGCTTTT	0	50	1
TCCGAATGGAACAAGAAAAGCATTTTTAAATT	0	65	0
TTCCATTCGGATAGAAACCTAATTGCTTGTTT	0	86	1
CTTGTTTGGTAGAAAAAACAAGCAATTAGGTT	0	101	0
TAGCACTGACGTAGGAAACTAATATGCCAAAA	0	203	1
AATGGAATGAAAAGAAAATGGATTTTTTGGCA	0	227	0
AAAAGAAAGGATAAGAAATGGAATGAAAAGAA	0	243	0
GGAGTGCGTAATAAAAAAGAAAGGATAAGAAA	0	257	0
 CTTTTCATTAAAGGAGAAAAA          	1	9	1
GCAAATAATGAGAAGAATTTGACCGCTTA   	2	7	0
GCAAAATGAGGGAAAAATTTGACCGCTTGTTT	2	37	1
CTTCTTTTCAAGAAAAAACAAGCGGTCAAATT	2	52	0
TTTTTCTTGAAAAGAAGCGTAAACTTCTTTCG	2	67	1
TAGCACTGACGTAGGAAACTAATATGCCACAT	2	153	1
GTAATAAAATGTAGAAAATTGGGAAAATAAAC	2	216	0
TGTTGAATATAAAATAAACAAAAATGCCCGCT	2	272	0
          * ****** ***
MAP Score: 4.44652

Motif 6
TTTGGTAGAAAAAACAAGCAATTAGGTTTCTATCC	0	94	0
CGGCACCCCGACTAAAAACTGTTGGTAAGTTTACG	0	133	0
ATACCCGTGAACCTGAAACAGTTAGCACTGACGTA	0	181	1
TTACGCACTCCCTTTAATCATTGAGGCGAGCA   	0	278	1
ATACCCGTGAACCTGAAACAGTTAGCACTGACGTA	2	131	1
CCCGCTATTCACTGTGAGCAATTAGCAGGTGTAAT	2	243	0
          **   ** ** ****
MAP Score: 3.83222

Motif 7
CCAACAGTTTTTAGTCGGGGTGCCGAAAGGCTGAGATG	0	143	1
CCTGAAACAGTTAGCACTGACGTAGGAAACTAATATGC	0	192	1
CTTTCGACTTTTAGTCGGGGTGCCGAAAGGCTGAGATG	2	93	1
CCTGAAACAGTTAGCACTGACGTAGGAAACTAATATGC	2	142	1
          ****    *  *  ****
MAP Score: 2.66296

Motif 8
ACCAACAGTTTTTAGTCGGGGTGCCGAAAGGCTGAGA	0	142	1
TGAAACAGTTAGCACTGACGTAGGAAACTAATATGCC	0	194	1
ACGCACTCCCTTTAATCATTGAGGCGAGCA       	0	280	1
       CTTTTCATTAAAGGAGAAAAA         	1	3	1
TCCCTCATTTTGCAAATAATGAGAAGAATTTGACCGC	2	13	0
TTGTTTTTTCTTGAAAAGAAGCGTAAACTTCTTTCGA	2	63	1
TCTTTCGACTTTTAGTCGGGGTGCCGAAAGGCTGAGA	2	92	1
TGAAACAGTTAGCACTGACGTAGGAAACTAATATGCC	2	144	1
TGTAATAAAATGTAGAAAATTGGGAAAATAAACAGGA	2	212	0
          ** * * *  * * ***
MAP Score: 1.31777