AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons008_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237548
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	murE	300	N-Acetylmuramoylalanylglutamyl DAP Ligase
#1	yabC_2	243	SAM-Dependent Methytransferase
#2	pbp2	300	PBP2-transglycolase/transpeptidase
#3	secA_2	183	Protein Translocase
#4	murF	300	Muramoyl-DAP Ligase

Motif 1
TCTATTGAAGTTTATGGAAGGGGGAGGTAAGGC	0	19	1
GGGATTTAGATTTGGGATAAAGGAGGCTTCTGT	0	62	1
AAATTTTATATTTCAGAGAAGAGTAAGAACTTT	0	114	1
CTCACTCTGATTTTTAAAAAATGCTTAAAGGAT	0	216	0
TAGAGGGCTTTTTATGAAAAAAGTTGTTTTTCA	0	259	1
ATCGAAGGCACTTAAGAAAAAAGCTCACCCCTA	1	105	1
CACTCTAAATTTTTTGATAGGGGTGAGCTTTTT	1	122	0
CTAGCGAGAATTTAAGATAAGGGAAGGCTTTCT	1	160	1
TCTCTGTAATTTTCAGACGAGAGTGAAGCTCAT	2	265	1
GAAAGAAGATTTTATGGTAAGCGAGAAGTGCGC	4	70	1
ATCTTAGTCGTTTTTGAGAGATGCAATTGCATT	4	124	1
TTTTAGTTCTCTTAAAAAAGAGGTTATGTAATC	4	155	1
          *** *** *** *
MAP Score: 13.1211

Motif 2
AATTTCGCTCTCCTGTTTCTACGAACAGAAGCCTC	0	84	0
CATAAAGTTCTTACTCTTCTCTGAAATATAAAATT	0	115	0
TTAAAAAACCGTCTCTATCTCTAGATGATAGTGCG	1	19	1
GGGAAGGCTTTCTTCTTTCTATGGAATCCTGTATC	1	180	1
ATGGAATCCTGTATCTTTGTCCTTATTTGAAGCCA	1	200	1
ACCTTCTCAAGTCTTTTTCTCTTGAGAAATTTTTT	2	37	1
TTCTTAAATATCGTGCTTCTTTTTATTATTGTATT	2	193	1
TAATGTGAGAGCATAGTTCTCTGTAATTTTCAGAC	2	248	1
TTTTTTAAATTTTTTATTCTATGGACTACAAAGCC	3	17	1
     ATGTCGTTTAATTCACTGTAATTACTAGAA	3	163	0
TACCATAAAATCTTCTTTCGCTTAAACTAAGGATT	4	54	0
CGAGAAGTGCGCATAATTCTAGAGACTAGGGAAAT	4	91	1
TGCAATTGCATTTTAGTTCTCTTAAAAAAGAGGTT	4	145	1
AAGGGTACTTGCATTCTTGTCTGCATTTTAAATAT	4	196	1
          ** *  ******  *
MAP Score: 11.254

Motif 3
GAAGCTGATTTCTGCTTTTTGTTATCTTCG	3	61	0
TTGATAGGGGTGAGCTTTTTTCTTAAGTGC	1	112	0
         ATCTGATTTTTTTAAATTTTT	3	1	1
ATGCTCTCACTCTGATTTTTAAAAAATGCT	0	224	0
TGCATTCTTGTCTGCATTTTAAATATAGTA	4	205	1
CTATTGAAAAACAACTTTTTTCATAAAAAG	0	266	0
ATGCCCCTAGAGGGCTTTTTATGAAAAAAG	0	252	1
TTTTAAATATAGTACTTTTTAGTGTAGGTC	4	221	1
AACTTTATGGACAGTTTTTTGTGATTGCTT	0	141	1
AGAGATAGAGACGGTTTTTTAAGGCCTCGC	1	11	0
ATCAAGACTATTGACTTTTTCCTAGACCGC	1	51	0
AGTTCGCCACTCTAAATTTTTTGATAGGGG	1	132	0
TTTTCTCTTGAGAAATTTTTTTTGTTTATT	2	51	1
CTATCTTGATTGAATTTTTTGTCGACCTAC	0	176	1
GAGAGATGCAATTGCATTTTAGTTCTCTTA	4	139	1
TCTGATTTTTTTAAATTTTTTATTCTATGG	3	11	1
          **********
MAP Score: 9.36305

Motif 4
TAGTGCGGTCTAGGAAAAAGTCAATAGTCTTGATCAGAAGC	1	47	1
TCTTTTTCTCTTGAGAAATTTTTTTTGTTTATTTTTATTAT	2	48	1
TTTTATTATTTAGAACATGATTTTTGGTTTTAATATGTTTT	2	80	1
ATGTTTTGATTGGACTAAAATTAGTTGTATTTTGCGAACTG	2	114	1
TAGATTTTGTTCGATTAGATTGACTATTCTTCTTAAATATC	2	164	1
ACTATTCTTCTTAAATATCGTGCTTCTTTTTATTATTGTAT	2	186	1
AATCAGCTTCTTGGGAACTTTTATTCGTTTTATTAAGTAAG	3	81	1
ACCAAAGGGGAGGATGAGAATCCTTAGTTTAAGCGAAAGAA	4	36	1
TTCTAGAGACTAGGGAAATCTTAGTCGTTTTTGAGAGATGC	4	107	1
CCTTATTAGGTTGATTACATAACCTCTTTTTTAAGAGAACT	4	159	0
          * **  *   *   * ** **
MAP Score: 8.9542

Motif 5
ATCAGAGTGAGAGCATGCCCCTAGAGGGCTTTTT	0	238	1
TTAAAAAACCGTCTCTATCTCTAGATGATAGTGC	1	19	1
TGATAGGGGTGAGCTTTTTTCTTAAGTGCCTTCG	1	107	0
ACCTTCTCAAGTCTTTTTCTCTTGAGAAATTTTT	2	37	1
CGATTAGATTGACTATTCTTCTTAAATATCGTGC	2	175	1
AATAATGTGAGAGCATAGTTCTCTGTAATTTTCA	2	246	1
TGGATATTATGAGCTTCACTCTCGTCTGAAAATT	2	272	0
      CCTCGGCCTTACCGCTTGGCTATGCCAC	4	4	1
AGCGAGAAGTGCGCATAATTCTAGAGACTAGGGA	4	89	1
TTTAGTGTAGGTCCATCCTTCTGGTAGGGAGTTC	4	238	1
          * ****  **** *
MAP Score: 7.72108

Motif 6
CTTCTGTTCGTAGAAACAGGAGAGCGAAATTTTATAT	0	88	1
AAGCATTTTTTAAAAATCAGAGTGAGAGCATGCCCCT	0	223	1
CGTCTCTATCTCTAGATGATAGTGCGGTCTAGGAAAA	1	28	1
AGAAAAAGACTTGAGAAGGTAGTGAGGAGCCATTTTT	2	20	0
CTCTGTAATTTTCAGACGAGAGTGAAGCTCATAATAT	2	266	1
AATTTTATATTTCAGAGAAGAGTAAGAACTTTATGGA	0	115	1
TGCGCATAATTCTAGAGACTAGGGAAATCTTAGTCGT	4	98	1
ATATTTAAAATGCAGACAAGAATGCAAGTACCCTTAT	4	194	0
TGGCTATGCCACCAAAGGGGAGGATGAGAATCCTTAG	4	26	1
AATCTAATCGAACAAAATCTAGAGAAGATACAGTTCG	2	148	0
TCACCCCTATCAAAAAATTTAGAGTGGCGAACTAGCG	1	129	1
          *  ***   *** * **
MAP Score: 6.18274

Motif 7
GTAGAAACAGGAGAGCGAAATTTTATATTTCAGA	0	97	1
CATGCCCCTAGAGGGCTTTTTATGAAAAAAGTTG	0	251	1
TTTGATAGGGGTGAGCTTTTTTCTTAAGTGCCTT	1	109	0
TAAGATAAGGGAAGGCTTTCTTCTTTCTATGGAA	1	172	1
GAAATAATGTGAGAGCATAGTTCTCTGTAATTTT	2	244	1
TTCGAGCCACGAGGGCTTTGTAGTCCATAGAATA	3	31	0
TAAGCGAGAAGTGCGCATAATTCTAGAGACTAGG	4	87	1
CATAGATGCTGTAGGCAAAATTAT          	4	286	1
          *** ** ** ** *
MAP Score: 5.54783

Motif 8
GCCCCTAGAGGGCTTTTTATGAAAAAAGTTGTTTTTCAATAGTCC	0	254	1
AAAGGTTCAGGCTTCTGATCAAGACTATTGACTTTTTCCTAGACC	1	53	0
CCACTCTAAATTTTTTGATAGGGGTGAGCTTTTTTCTTAAGTGCC	1	111	0
GAACTAGCGAGAATTTAAGATAAGGGAAGGCTTTCTTCTTTCTAT	1	157	1
ACCTTCTCAAGTCTTTTTCTCTTGAGAAATTTTTTTTGTTTATTT	2	37	1
TTTATTTTTATTATTTAGAACATGATTTTTGGTTTTAATATGTTT	2	75	1
AAAATTAGTTGTATTTTGCGAACTGTATCTTCTCTAGATTTTGTT	2	130	1
ATCTTCTCTAGATTTTGTTCGATTAGATTGACTATTCTTCTTAAA	2	156	1
      ATCTGATTTTTTTAAATTTTTTATTCTATGGACTACAAA	3	4	1
GCAGAAATCAGCTTCTTGGGAACTTTTATTCGTTTTATTAAGTAA	3	76	1
       ATGTCGTTTAATTCACTGTAATTACTAGAATACCATCT	3	155	0
CCATAAAATCTTCTTTCGCTTAAACTAAGGATTCTCATCCTCCCC	4	42	0
AATCTTAGTCGTTTTTGAGAGATGCAATTGCATTTTAGTTCTCTT	4	123	1
ATTCTTGTCTGCATTTTAAATATAGTACTTTTTAGTGTAGGTCCA	4	208	1
AGGGAGTTCAGACTTTCTAAAACCATAGATGCTGTAGGCAAAATT	4	263	1
          *  ***     *   **  *  * *
MAP Score: 3.94677

Motif 9
GAGACGGTCTATTGAAGTTTATGGAAGGGGGAGGTAAGG	0	12	1
AGAGCGAAATTTTATATTTCAGAGAAGAGTAAGAACTTT	0	108	1
ACCGTCTCTATCTCTAGATGATAGTGCGGTCTAGGAAAA	1	26	1
AGGGGTGAGCTTTTTTCTTAAGTGCCTTCGATAAGGAGA	1	98	0
CCACTCTAAATTTTTTGATAGGGGTGAGCTTTTTTCTTA	1	117	0
ACTAGCGAGAATTTAAGATAAGGGAAGGCTTTCTTCTTT	1	159	1
GGGAAGGCTTTCTTCTTTCTATGGAATCCTGTATCTTTG	1	180	1
TTTGTCCTTATTTGAAGCCAAGAGCTTAGGAAATTCTT 	1	215	1
TTCTCTGTAATTTTCAGACGAGAGTGAAGCTCATAATAT	2	264	1
TTTTTTAAATTTTTTATTCTATGGACTACAAAGCCCTCG	3	17	1
CGAAAGAAGATTTTATGGTAAGCGAGAAGTGCGCATAAT	4	69	1
TGCGCATAATTCTAGAGACTAGGGAAATCTTAGTCGTTT	4	98	1
          ***  ** * ** *    *
MAP Score: 2.29739

Motif 10
  ATGAGACGGTCTATTGAAGTTTATGGAA	0	8	1
GTCTATTGAAGTTTATGGAAGGGGGAGGTA	0	18	1
AAATTTTATATTTCAGAGAAGAGTAAGAAC	0	114	1
AGAGTAAGAACTTTATGGACAGTTTTTTGT	0	133	1
TGATAGTGCGGTCTAGGAAAAAGTCAATAG	1	44	1
GCTTTCTTCTTTCTATGGAATCCTGTATCT	1	186	1
AAGTCTTTTTCTCTTGAGAAATTTTTTTTG	2	45	1
AAATTTTTTATTCTATGGACTACAAAGCCC	3	23	1
AGAAATCAGCTTCTTGGGAACTTTTATTCG	3	78	1
GTGCGCATAATTCTAGAGACTAGGGAAATC	4	97	1
          **********
MAP Score: 0.839312

Motif 11
GGTCTATTGAAGTTTATGGAAGGGGGAGGTAAGGCTGTGT	0	17	1
TTGGGGATTTAGATTTGGGATAAAGGAGGCTTCTGTTCGT	0	59	1
TCGACCTACGAGTAAAGAAATCCTTTAAGCATTTTTTAAA	0	197	1
CATTTTTTAAAAATCAGAGTGAGAGCATGCCCCTAGAGGG	0	226	1
CATCTAGAGATAGAGACGGTTTTTTAAGGCCTCGCC    	1	6	0
GTGCCTTCGATAAGGAGAAAAGGTTCAGGCTTCTGATCAA	1	76	0
AACTAGCGAGAATTTAAGATAAGGGAAGGCTTTCTTCTTT	1	158	1
GCTTCAAATAAGGACAAAGATACAGGATTCCATAGAAAGA	1	193	0
CCTTATTTGAAGCCAAGAGCTTAGGAAATTCTT       	1	220	1
ATTTCTCAAGAGAAAAAGACTTGAGAAGGTAGTGAGGAGC	2	27	0
ATAATTCTAGAGACTAGGGAAATCTTAGTCGTTTTTGAGA	4	103	1
TAGTTCTCTTAAAAAAGAGGTTATGTAATCAACCTAATAA	4	158	1
GTAATCAACCTAATAAGGGTACTTGCATTCTTGTCTGCAT	4	182	1
AGACTTTCTAAAACCATAGATGCTGTAGGCAAAATTAT  	4	272	1
          **   * **     * ****
MAP Score: 0.579183

Motif 12
TCACTCTGATTTTTAAAAAATGCTTAAAGGAT	0	216	0
AGAGGGCTTTTTATGAAAAAAGTTGTTTTTCA	0	260	1
CTCCAGGGACTATTGAAAAACAACTTTTTTCA	0	273	0
GATAGTGCGGTCTAGGAAAAAGTCAATAGTCT	1	45	1
GTGCCTTCGATAAGGAGAAAAGGTTCAGGCTT	1	84	0
TCGAAGGCACTTAAGAAAAAAGCTCACCCCTA	1	106	1
AAAAAATTTCTCAAGAGAAAAAGACTTGAGAA	2	40	0
ATAATAAAAATAAACAAAAAAAATTTCTCAAG	2	57	0
ATTAGTTGTATTTTGCGAACTGTATCTTCTCT	2	133	1
AGCACGATATTTAAGAAGAATAGTCAATCTAA	2	178	0
TCGAGTATGGTATTGAGAAACGTTCTCGTAAA	3	123	1
AATCCTTAGTTTAAGCGAAAGAAGATTTTATG	4	54	1
TCTTAGTCGTTTTTGAGAGATGCAATTGCATT	4	125	1
AACCTCTTTTTTAAGAGAACTAAAATGCAATT	4	148	0
          * ******** *
MAP Score: 0.512538