AlignACE 3.0 10/20/99
AlignACE2 -i HY/HY_operons018_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252607
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hsdM_1	300	TYPE I RESTRICTION ENZYME (MODIFICATION SUBUNIT)
#1	jhp0742	48	putative
#2	hsdR_2	300	TYPE I RESTRICTION ENZYME (RESTRICTION SUBUNIT)
#3	hsdM_2	178	TYPE I RESTRICTION ENZYME (MODIFICATION SUBUNIT)
#4	hsdM_3_hsdR_3	70	hsdM_3: TYPE I RESTRICTION ENZYME (MODIFICATION SUBUNIT), hsdR_3: TYPE I RESTRICTION ENZYME (RESTRICTION SUBUNIT)

Motif 1
CAATAACGATCGAGCTTATGTGATCACGCA	0	11	1
CGATTGTGAAGTCGCTTATGCGTGATCACA	0	29	0
CTTTTTTGAGCGCGCTTAAAAGCGTGAAAA	0	88	0
AAGATTTCTTGACGCTTAAAAATACGCTCA	0	125	0
CTTTTAAGGAGGGGTTTTTGTTGAAAGCGT	0	202	0
TTTCCTTGATGGTGGTTTTGCGTGAGTTCG	0	275	0
GGGAGTTTATCGCGCTTTTACAAAAACAAG	2	23	1
TTTTTAATCTCGCGCTTGAGAACGGGAAAA	2	233	1
          GGCGTTTCTATGGATATTTT	2	290	0
GGTTTTGTTTGGCGGTTTTAGCACGCCCCT	3	126	0
TGTTTTGATTGGCGGTTTTGTTTGGCGGTT	3	139	0
ACACAAAAAAGGGGCTTATCTC        	3	166	1
GCGTTCTTAAGGGGTTTATG          	4	0	0
AACAAAATAGGGCGGTTAAAA         	4	59	1
          **********
MAP Score: 15.9547

Motif 2
TCTCATGGAAGAAAACATTTCTAAGGGAATTTTCACGC	0	59	1
AAGCGCGCTCAAAAAAGCTATTGATGAGCGTATTTTTA	0	101	1
TAAGCGTCAAGAAATCTTAAACGAAGAAGATACCCTAA	0	137	1
AAGATACCCTAAAAACTGCCATAAAAGTAGAATTAAGG	0	163	1
GCTTTCAACAAAAACCCCTCCTTAAAAGATTTAGAAAA	0	204	1
ATTTATCGCTCAAACCCTTTTTAACGAACTCACGCAAA	0	251	1
CGAACTCACGCAAAACCACCATCAAGGAAATTTGA   	0	275	1
CGCGCTTTTACAAAAACAAGGCTATGAATTTAAAAAAA	2	33	1
TGAATTTAAAAAAATCCACAACGAAAAAGAATTAAAAG	2	57	1
AAAAAGAATTAAAAGACAATTTAAAAGAGCAGTTAGAA	2	80	1
CATCGCTAATAAAAACGAAGATTACAAGGCTAAAACAA	2	174	1
CAAAAACATTAAAATCATTGATAAGAAAAATATCCATA	2	264	1
         TCAAACCCCTTTTAAAAATGTCTTTTAAA	3	1	1
CCCACAAATACAGAGCAAACGCAAGGGATAAAAAAATA	3	61	1
AACCGCCAATCAAAACACAAAAAAGGGGCTTATCTC  	3	152	1
TAAAGCGGTAAAAAGCGTTCTTAAGGGGTTTATG    	4	6	0
          **** *     * * ***
MAP Score: 14.9028

Motif 3
GCGGTAAAAAGCGTTCTTAAGGGGTTTATG   	4	7	0
GGGAATTTTCACGCTTTTAAGCGCGCTCAAAAA	0	83	1
TTTTTAAAAGACATTTTTAAAAGGGGTTTGA  	3	8	0
AGCTATAATCCCATTTTTAAAAGACATTTTTAA	3	21	0
TACTTTTATGGCAGTTTTTAGGGTATCTTCTTC	0	159	0
CTCATCAATAGCTTTTTTGAGCGCGCTTAAAAG	0	96	0
ATGGAAGAAAACATTTCTAAGGGAATTTTCACG	0	63	1
ATTGATGAGCGTATTTTTAAGCGTCAAGAAATC	0	120	1
TATCGCTCAAACCCTTTTTAACGAACTCACGCA	0	254	1
TTTGGTTTTCCCGTTCTCAAGCGCGAGATTAAA	2	235	0
CAACAAAAACCCCTCCTTAAAAGATTTAGAAAA	0	209	1
TAAGCGTCAAGAAATCTTAAACGAAGAAGATAC	0	137	1
TTTTCTAACTGCTCTTTTAAATTGTCTTTTAAT	2	87	0
TGCTATAATGAAACCTTTAAGGGGCGTGCTAAA	3	107	1
  GAGATAAGCCCCTTTTTTGTGTTTTGATTGG	3	157	0
          **  ******* *
MAP Score: 14.63

Motif 4
TTCTAAGGGAATTTTCACGCTTTTAAGCGCGC	0	77	1
TCAATAGCTTTTTTGAGCGCGCTTAAAAGCGT	0	93	0
AAAGAAACAGAATTTATCGCTCAAACCCTTTT	0	240	1
GCTCAAACCCTTTTTAACGAACTCACGCAAAA	0	258	1
CTAGAAAGGGAGTTTATCGCGCTTTTACAAAA	2	16	1
TAACGATCATTGTTTCACGCCCAAAGAATGGG	2	123	1
AAGATCCGATTTTTAATCTCGCGCTTGAGAAC	2	224	1
GATTATAGCTTATTTACCCCACAAATACAGAG	3	44	1
GAATATTATTTTTTTATCCCTTGCGTTTGCTC	3	73	0
GTTTGGCGGTTTTAGCACGCCCCTTAAAGGTT	3	118	0
TTAAGAACGCTTTTTACCGCTTTATATTATAA	4	20	1
          TTTTAACCGCCCTATTTTGTTT	4	58	0
          ****** *** *
MAP Score: 14.3448

Motif 5
GATCGAGCTTATGTGATCACGCATAAGCGACTTCACAAT	0	18	1
CGTCTCATGGAAGAAAACATTTCTAAGGGAATTTTCACG	0	57	1
AAAGCTATTGATGAGCGTATTTTTAAGCGTCAAGAAATC	0	114	1
AAAAACTGCCATAAAAGTAGAATTAAGGGACGCTTTCAA	0	173	1
TTTCTTTTTCTAAATCTTTTAAGGAGGGGTTTTTGTTGA	0	208	0
AAAAAGAATTAAAAGACAATTTAAAAGAGCAGTTAGAAA	2	80	1
TTTATTAGCGATGAATTGAAAATAAAGAGTGTCCCATTC	2	148	0
ACAAGGCTAAAACAAGAAAGATCCAAGAAGATCCGATTT	2	197	1
ACCAAAAACATTAAAATCATTGATAAGAAAAATATCCAT	2	262	1
CCATTTTTAAAAGACATTTTTAAAAGGGGTTTGA     	3	5	0
ACCCCACAAATACAGAGCAAACGCAAGGGATAAAAAAAT	3	59	1
ATTCTTTGCTATAATGAAACCTTTAAGGGGCGTGCTAAA	3	101	1
AAAACCGCCAATCAAAACACAAAAAAGGGGCTTATCTC 	3	150	1
ATAAAGCGGTAAAAAGCGTTCTTAAGGGGTTTATG    	4	6	0
TTTTGTTTTTAGGATTATAATATAAAGCGGTAAAAAGCG	4	27	0
          ****    *     *****
MAP Score: 9.77802

Motif 6
 ACAATAACGATCGAGCTTATGTGATCACGCA	0	9	1
AGCTTATGTGATCACGCATAAGCGACTTCACA	0	23	1
TAAGGGAATTTTCACGCTTTTAAGCGCGCTCA	0	80	1
ATAGCTTTTTTGAGCGCGCTTAAAAGCGTGAA	0	90	0
GAAACAGAATTTATCGCTCAAACCCTTTTTAA	0	243	1
CAGCCTTACATTCTAGCGCAAATTTTAGTAAA	1	17	1
GAAAGGGAGTTTATCGCGCTTTTACAAAAACA	2	19	1
CGATCATTGTTTCACGCCCAAAGAATGGGACA	2	126	1
CCGATTTTTAATCTCGCGCTTGAGAACGGGAA	2	229	1
AAAAATGGGATTATAGCTTATTTACCCCACAA	3	36	1
AGAACGCTTTTTACCGCTTTATATTATAATCC	4	23	1
          *** *** ****
MAP Score: 4.53707

Motif 7
AGCTTATGTGATCACGCATAAGCGACTTCACAATCGTCTCATG	0	23	1
TAAGGGAATTTTCACGCTTTTAAGCGCGCTCAAAAAAGCTATT	0	80	1
CAAGAAATCTTAAACGAAGAAGATACCCTAAAAACTGCCATAA	0	144	1
GAAACAGAATTTATCGCTCAAACCCTTTTTAACGAACTCACGC	0	243	1
CTTTTTAACGAACTCACGCAAAACCACCATCAAGGAAATTTGA	0	267	1
CAGCCTTACATTCTAGCGCAAATTTTAGTAAAATACGCATC  	1	17	1
GAAAGGGAGTTTATCGCGCTTTTACAAAAACAAGGCTATGAAT	2	19	1
TTTAAAAAAATCCACAACGAAAAAGAATTAAAAGACAATTTAA	2	61	1
CGATCATTGTTTCACGCCCAAAGAATGGGACACTCTTTATTTT	2	126	1
ATCGCTAATAAAAACGAAGATTACAAGGCTAAAACAAGAAAGA	2	175	1
CCGATTTTTAATCTCGCGCTTGAGAACGGGAAAACCAAAAACA	2	229	1
AAAAATGGGATTATAGCTTATTTACCCCACAAATACAGAGCAA	3	36	1
GGGCGTGCTAAAACCGCCAAACAAAACCGCCAATCAAAACACA	3	128	1
          * * ***  **         ***
MAP Score: 3.57156