AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions015_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236739
 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
ATTTAAAAATGCTTTTCTTGTTCCATTCGGAT	0	66	1
AAACCTAATTGCTTGTTTTTTCTACCAAACAA	0	100	1
GTAAGTTTACGCTTGTTTGGTAGAAAAAACAA	0	112	0
CTACGTCAGTGCTAACTGTTTCAGGTTCACGG	0	185	0
GGATTTTTTGGCATATTAGTTTCCTACGTCAG	0	208	0
GCCAAAAAATCCATTTTCTTTTCATTCCATTT	0	228	1
CATTTCTTATCCTTTCTTTTTTATTACGCACT	0	255	1
AAATTTGACCGCTTGTTTTTTCTTGAAAAGAA	2	51	1
CTACGTCAGTGCTAACTGTTTCAGGTTCACGG	2	135	0
TGAATATGTGGCATATTAGTTTCCTACGTCAG	2	158	0
ACATATTCAACCTTTCTCTATCACGATTTTAT	2	181	1
ACGATTTTATCCTGTTTATTTTCCCAATTTTC	2	203	1
TGAATAGCGGGCATTTTTGTTTATTTTATATT	2	267	1
          **** ** ****
MAP Score: 13.3074

Motif 2
AGTTTTTAGTCGGGGTGCCGAAAGGCTGAGATGATACCC	0	148	1
AGATGATACCCGTGAACCTGAAACAGTTAGCACTGACGT	0	176	1
GACTTTTAGTCGGGGTGCCGAAAGGCTGAGATGATACCC	2	98	1
AGATGATACCCGTGAACCTGAAACAGTTAGCACTGACGT	2	126	1
AGGATAAAATCGTGATAGAGAAAGGTTGAATATGTGGCA	2	177	0
          ** *   * ****   * *
MAP Score: 11.1629

Motif 3
GATCGTACAACTGATATTAGATAATAATTTTAG   	0	7	0
TAAGTTTACGCTTGTTTGGTAGAAAAAACAAGCAAT	0	107	0
ACGTAGGAAACTAATATGCCAAAAAATCCATTTTCT	0	211	1
AAATTTTTCCCTCATTTTGCAAATAATGAGAAGAAT	2	21	0
GAAGTTTACGCTTCTTTTCAAGAAAAAACAAGCGGT	2	58	0
ACGTAGGAAACTAATATGCCACATATTCAACCTTTC	2	161	1
        TCCTTGTGTTGAATATAAAATAAACAAA	2	282	0
          **  * **  * ****
MAP Score: 7.86119

Motif 4
TGTATCTTAGCAAGAGAAATTTAAAAATGCTTTTC	0	48	1
GTTTTTTCTACCAAACAAGCGTAAACTTACCAACA	0	114	1
TGAGATGATACCCGTGAACCTGAAACAGTTAGCAC	0	174	1
TTAGCACTGACGTAGGAAACTAATATGCCAAAAAA	0	202	1
GATAAGAAATGGAATGAAAAGAAAATGGATTTTTT	0	231	0
GTTTTTTCTTGAAAAGAAGCGTAAACTTCTTTCGA	2	65	1
TGAGATGATACCCGTGAACCTGAAACAGTTAGCAC	2	124	1
TTAGCACTGACGTAGGAAACTAATATGCCACATAT	2	152	1
     TCCTTGTGTTGAATATAAAATAAACAAAAA	2	280	0
          *  * *** ** ***
MAP Score: 7.66528

Motif 5
TTGTTTGGTAGAAAAAACAAGCAATTAGGTT	0	101	0
TCGGGGTGCCGAAAGGCTGAGATGATACCCG	0	157	1
TAATAAAAAAGAAAGGATAAGAAATGGAATG	0	250	0
TTCTTTTCAAGAAAAAACAAGCGGTCAAATT	2	52	0
GTTTTTTCTTGAAAAGAAGCGTAAACTTCTT	2	65	1
TCGGGGTGCCGAAAGGCTGAGATGATACCCG	2	107	1
          ******* ***
MAP Score: 7.61937

Motif 6
ATTTAAAAATGCTTTTCTTGTTCCATTCGGAT	0	66	1
AAACCTAATTGCTTGTTTTTTCTACCAAACAA	0	100	1
TGTTGGTAAGTTTACGCTTGTTTGGTAGAAAA	0	117	0
ACGGGTATCATCTCAGCCTTTCGGCACCCCGA	0	157	0
AAAATGGATTTTTTGGCATATTAGTTTCCTAC	0	213	0
AAAAAATCCATTTTCTTTTCATTCCATTTCTT	0	231	1
TCATTCCATTTCTTATCCTTTCTTTTTTATTA	0	249	1
         TTTTTCTCCTTTAATGAAAAG  	1	8	0
GCGGTCAAATTCTTCTCATTATTTGCAAAATG	2	13	1
AAATTTGACCGCTTGTTTTTTCTTGAAAAGAA	2	51	1
TCGAAAGAAGTTTACGCTTCTTTTCAAGAAAA	2	68	0
ACGGGTATCATCTCAGCCTTTCGGCACCCCGA	2	107	0
TCTATCACGATTTTATCCTGTTTATTTTCCCA	2	197	1
ATAGCGGGCATTTTTGTTTATTTTATATTCAA	2	270	1
          **** **** **
MAP Score: 5.79461

Motif 7
AATTTAAAAATGCTTTTCTTGTTCCATTCGG	0	65	1
GAAACCTAATTGCTTGTTTTTTCTACCAAAC	0	99	1
GGTAAGTTTACGCTTGTTTGGTAGAAAAAAC	0	114	0
CATTTCTTATCCTTTCTTTTTTATTACGCAC	0	255	1
CAAATTCTTCTCATTATTTGCAAAATGAGGG	2	18	1
AAAATTTGACCGCTTGTTTTTTCTTGAAAAG	2	50	1
AAGAAGTTTACGCTTCTTTTCAAGAAAAAAC	2	65	0
GATTTTATCCTGTTTATTTTCCCAATTTTCT	2	205	1
          TCCTTGTGTTGAATATAAAAT	2	289	0
          ***** *****
MAP Score: 5.77907

Motif 8
ACCTAATTGCTTGTTTTTTCTACCAAACAAG	0	102	1
AACTTACCAACAGTTTTTAGTCGGGGTGCCG	0	137	1
TTCTTATCCTTTCTTTTTTATTACGCACTCC	0	258	1
ATTTGACCGCTTGTTTTTTCTTGAAAAGAAG	2	53	1
CGATTTTATCCTGTTTATTTTCCCAATTTTC	2	204	1
GCGGGCATTTTTGTTTATTTTATATTCAACA	2	273	1
          ********* *
MAP Score: 5.10196

Motif 9
TTAAAAATGCTTTTCTTGTTCCATTCGGATA	0	68	1
CTAATTGCTTGTTTTTTCTACCAAACAAGCG	0	104	1
CTGTTGGTAAGTTTACGCTTGTTTGGTAGAA	0	119	0
TCATCTCAGCCTTTCGGCACCCCGACTAAAA	0	151	0
AGGTTCACGGGTATCATCTCAGCCTTTCGGC	0	164	0
AGTGCTAACTGTTTCAGGTTCACGGGTATCA	0	179	0
TTGACCGCTTGTTTTTTCTTGAAAAGAAGCG	2	55	1
GTCGAAAGAAGTTTACGCTTCTTTTCAAGAA	2	70	0
TCATCTCAGCCTTTCGGCACCCCGACTAAAA	2	101	0
AGGTTCACGGGTATCATCTCAGCCTTTCGGC	2	114	0
AGTGCTAACTGTTTCAGGTTCACGGGTATCA	2	129	0
ATTTTATCCTGTTTATTTTCCCAATTTTCTA	2	206	1
          ***** *****
MAP Score: 4.86881

Motif 10
CGTTGTATCTTAGCAAGAGAAATTTAAAAAT	0	45	1
TCCATTCGGATAGAAACCTAATTGCTTGTTT	0	87	1
AGCACTGACGTAGGAAACTAATATGCCAAAA	0	204	1
TAAGAAATGGAATGAAAAGAAAATGGATTTT	0	233	0
ATAAAAAAGAAAGGATAAGAAATGGAATGAA	0	248	0
TTTTTCTTGAAAAGAAGCGTAAACTTCTTTC	2	67	1
AGCACTGACGTAGGAAACTAATATGCCACAT	2	154	1
TGTAGAAAATTGGGAAAATAAACAGGATAAA	2	208	0
          ****** ****
MAP Score: 0.697001