AlignACE 3.0 10/20/99
AlignACE2 -i HY/HY_fusions007_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251563
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	thiM	92	HYDROXYETHYLTHIAZOLE KINASE
#1	hsdR_2	300	TYPE I RESTRICTION ENZYME (RESTRICTION SUBUNIT)
#2	jhp1207	300	putative TRANSCRIPTIONAL REGULATOR

Motif 1
TTAAAAGACAATTTAAAAGAGCAGTTAGAA	1	88	1
CTCACAAATCTTTTAAAAACAAATTTTATA	2	222	1
AACGAAAAAGAATTAAAAGACAATTTAAAA	1	76	1
AGCCTTGTTTTTGTAAAAGCGCGATAAACT	1	26	0
ATTAATCGCCATTCAAAATCACAGATATTT	2	158	1
AAACTTCTAAAAATAAAAACCTACAGAGTG	2	49	1
AAAAGAGCAGTTAGAAAAGCTTAACGATCA	1	102	1
TTTTCTTGTAAAATAAAAGAAAGTTTAAGG	0	63	1
AAGGCTATGAATTTAAAAAAATCCACAACG	1	50	1
AATTCATCGCTAATAAAAACGAAGATTACA	1	170	1
CAAGTTCCCATAATAAAAACTTCTAAAAAT	2	33	1
AAACCAAAAACATTAAAATCATTGATAAGA	1	260	1
TTGCATCAAATTTCAAAAACAGCGCCGCTC	0	27	1
TTGAAATTTGATGCAAAAGCGTTCAACAAC	0	13	0
TTGAACGCTGTATTAAAATATCTGTGATTT	2	173	0
TTAGCGATGAATTGAAAATAAAGAGTGTCC	1	153	0
CAAGCGCGAGATTAAAAATCGGATCTTCTT	1	221	0
TTTTATTTTACAAGAAAATCCATTGAGCGG	0	51	0
          **********
MAP Score: 13.4756

Motif 2
CTTTTGCATCAAATTTCAAAAACAGCGCCGCTCAATGGATTTTC	0	24	1
AATGGATTTTCTTGTAAAATAAAAGAAAGTTTAAGGAGGTTCGT	0	57	1
GTTTATCGCGCTTTTACAAAAACAAGGCTATGAATTTAAAAAAA	1	27	1
CAAGGCTATGAATTTAAAAAAATCCACAACGAAAAAGAATTAAA	1	49	1
AATTAAAAGACAATTTAAAAGAGCAGTTAGAAAAGCTTAACGAT	1	86	1
TTCAATTCATCGCTAATAAAAACGAAGATTACAAGGCTAAAACA	1	167	1
CGAAGATTACAAGGCTAAAACAAGAAAGATCCAAGAAGATCCGA	1	189	1
AAAACCAAAAACATTAAAATCATTGATAAGAAAAATATCCATAG	1	259	1
CCATAATAAAAACTTCTAAAAATAAAAACCTACAGAGTGAGATG	2	40	1
AAAGGATAGCCAGTCTTAAACAACACAAAGGCAATACAAGCCCT	2	106	1
CATTAATCGCCATTCAAAATCACAGATATTTTAATACAGCGTTC	2	157	1
ACAGCGTTCAATTTTTGAAACAAGAGTTCACTCACAAATCTTTT	2	192	1
ACTCACAAATCTTTTAAAAACAAATTTTATACCATATTGTGAGC	2	221	1
          *  **  *****          **
MAP Score: 9.962

Motif 3
ATTTGATGCAAAAGCGTTCAACAACAAA        	0	2	0
CGCTTTTGCATCAAATTTCAAAAACAGCGCCGCTCA	0	22	1
CCACAACGAAAAAGAATTAAAAGACAATTTAAAAGA	1	72	1
GAGCAGTTAGAAAAGCTTAACGATCATTGTTTCACG	1	106	1
AAAGAATGGGACACTCTTTATTTTCAATTCATCGCT	1	145	1
CCAAGAAGATCCGATTTTTAATCTCGCGCTTGAGAA	1	219	1
CGGGAAAACCAAAAACATTAAAATCATTGATAAGAA	1	255	1
CAAAGGATAGCCAGTCTTAAACAACACAAAGGCAAT	2	105	1
AAGGCAATACAAGCCCTATAATATCATTAATCGCCA	2	133	1
ATATCATTAATCGCCATTCAAAATCACAGATATTTT	2	153	1
ATTTTTGAAACAAGAGTTCACTCACAAATCTTTTAA	2	202	1
GTTCACTCACAAATCTTTTAAAAACAAATTTTATAC	2	217	1
      TTTTACACTCCTAAAATTCAATTCAACACG	2	280	0
          ***   ** **  ***
MAP Score: 7.92683

Motif 4
TGCATCAAATTTCAAAAACAGCGCCGCTCAAT	0	28	1
AGGCTATGAATTTAAAAAAATCCACAACGAAA	1	51	1
TTAAAAGACAATTTAAAAGAGCAGTTAGAAAA	1	88	1
CACTCTTTATTTTCAATTCATCGCTAATAAAA	1	156	1
TTAATCGCCATTCAAAATCACAGATATTTTAA	2	159	1
ATCACAGATATTTTAATACAGCGTTCAATTTT	2	175	1
TCACAAATCTTTTAAAAACAAATTTTATACCA	2	223	1
CACTCCTAAAATTCAATTCAACACGCATTCTA	2	273	0
          *** ****** *
MAP Score: 3.58285

Motif 5
TTTGTTGTTGAACGCTTTTGCATCAAATTTCAAAAACAGCGCCGCT	0	10	1
AGCGCCGCTCAATGGATTTTCTTGTAAAATAAAAGAAAGTTTAAGG	0	47	1
GCGCAGCTAGAAAGGGAGTTTATCGCGCTTTTACAAAAACAAGGCT	1	10	1
CCACAACGAAAAAGAATTAAAAGACAATTTAAAAGAGCAGTTAGAA	1	72	1
AGCAGTTAGAAAAGCTTAACGATCATTGTTTCACGCCCAAAGAATG	1	107	1
ACGCCCAAAGAATGGGACACTCTTTATTTTCAATTCATCGCTAATA	1	139	1
CGAAGATTACAAGGCTAAAACAAGAAAGATCCAAGAAGATCCGATT	1	189	1
GCGCTTGAGAACGGGAAAACCAAAAACATTAAAATCATTGATAAGA	1	244	1
TTATGATTACAAAGGATAGCCAGTCTTAAACAACACAAAGGCAATA	2	96	1
AAACAACACAAAGGCAATACAAGCCCTATAATATCATTAATCGCCA	2	123	1
GTTCACTCACAAATCTTTTAAAAACAAATTTTATACCATATTGTGA	2	217	1
TTCGTGTTAGAATGCGTGTTGAATTGAATTTTAGGAGTGTAAAA  	2	266	1
          ** ** *    *      **  *  *
MAP Score: 3.48369

Motif 6
   TTTGTTGTTGAACGCTTTTGCATCAAATTTCAAAAACAGCGC	0	7	1
         AACGAACCTCCTTAAACTTTCTTTTATTTTACAAGA	0	66	0
  GCGCAGCTAGAAAGGGAGTTTATCGCGCTTTTACAAAAACAAG	1	8	1
AATCCACAACGAAAAAGAATTAAAAGACAATTTAAAAGAGCAGTT	1	69	1
AGAGCAGTTAGAAAAGCTTAACGATCATTGTTTCACGCCCAAAGA	1	105	1
TAAAACAAGAAAGATCCAAGAAGATCCGATTTTTAATCTCGCGCT	1	204	1
ATCATTAATCGCCATTCAAAATCACAGATATTTTAATACAGCGTT	2	155	1
GAGTTCACTCACAAATCTTTTAAAAACAAATTTTATACCATATTG	2	215	1
CTTTCGTGTTAGAATGCGTGTTGAATTGAATTTTAGGAGTGTAAA	2	264	1
          *  ** *   *  *      *** *
MAP Score: 1.92007

Motif 7
TTGTAAAATAAAAGAAAGTTTAAGGAGGTT	0	68	1
GCGCAGCTAGAAAGGGAGTTTATCGCGCTT	1	10	1
ATCCACAACGAAAAAGAATTAAAAGACAAT	1	70	1
AAAAGAATTAAAAGACAATTTAAAAGAGCA	1	81	1
GACAATTTAAAAGAGCAGTTAGAAAAGCTT	1	94	1
TAAACAACACAAAGGCAATACAAGCCCTAT	2	122	1
CAATTTTTGAAACAAGAGTTCACTCACAAA	2	200	1
CAAATCTTTTAAAAACAAATTTTATACCAT	2	226	1
          **********
MAP Score: 1.59508