AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons008_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237573
 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	psdD	150	Phosphatidylserine Decarboxylase
#4	CPn0840	59	CT700 hypothetical protein
#5	secA_2	183	Protein Translocase
#6	murF	300	Muramoyl-DAP Ligase

Motif 1
ATAAAGTTCTTACTCTTCTCTGAAATATAAAATTTC	0	113	0
GAAGAAAGCCTTCCCTTATCTTAAATTCTCGCTAGT	1	159	0
GGAAGGCTTTCTTCTTTCTATGGAATCCTGTATCTT	1	181	1
CCTGTATCTTTGTCCTTATTTGAAGCCAAGAGCTTA	1	207	1
CCTTCTCAAGTCTTTTTCTCTTGAGAAATTTTTTTT	2	38	1
AGAAATTTTTTTTGTTTATTTTTATTATTTAGAACA	2	61	1
CTAGATTTTGTTCGATTAGATTGACTATTCTTCTTA	2	163	1
TCTTAAATATCGTGCTTCTTTTTATTATTGTATTTA	2	194	1
AATGTGAGAGCATAGTTCTCTGTAATTTTCAGACGA	2	249	1
TTTTGACTTTTATCTCTCTTTGCAATACCAAAAAAA	4	23	0
         ATCTGATTTTTTTAAATTTTTTATTCT	5	1	1
TTTTTAAATTTTTTATTCTATGGACTACAAAGCCCT	5	18	1
TCTTGGGAACTTTTATTCGTTTTATTAAGTAAGATC	5	89	1
    ATGTCGTTTAATTCACTGTAATTACTAGAATA	5	161	0
ACCATAAAATCTTCTTTCGCTTAAACTAAGGATTCT	6	52	0
GCAATTGCATTTTAGTTCTCTTAAAAAAGAGGTTAT	6	146	1
ATGCAAGTACCCTTATTAGGTTGATTACATAACCTC	6	174	0
AGGGTACTTGCATTCTTGTCTGCATTTTAAATATAG	6	197	1
GCATTTTAAATATAGTACTTTTTAGTGTAGGTCCAT	6	218	1
          * *  **** ** * *
MAP Score: 13.5443

Motif 2
TCTATTGAAGTTTATGGAAGGGGGAGGTAAGGCTGT	0	19	1
GGGATTTAGATTTGGGATAAAGGAGGCTTCTGTTCG	0	62	1
AAATTTTATATTTCAGAGAAGAGTAAGAACTTTATG	0	114	1
TAGAGGGCTTTTTATGAAAAAAGTTGTTTTTCAATA	0	259	1
CACTCTAAATTTTTTGATAGGGGTGAGCTTTTTTCT	1	119	0
CTAGCGAGAATTTAAGATAAGGGAAGGCTTTCTTCT	1	160	1
TCTCTGTAATTTTCAGACGAGAGTGAAGCTCATAAT	2	265	1
GAATACCAAGTTTTAGATTAAAGAGGTGAAAGGAGT	3	42	1
GAAAGAAGATTTTATGGTAAGCGAGAAGTGCGCATA	6	70	1
ATCTTAGTCGTTTTTGAGAGATGCAATTGCATTTTA	6	124	1
          ***  ** *** *  *
MAP Score: 12.4937

Motif 3
TATGGACAGTTTTTTGTGATTGCTTGTATACT	0	146	1
TCTTGAGAAATTTTTTTTGTTTATTTTTATTA	2	56	1
TTTTTGTTTATTTTTATTATTTAGAACATGAT	2	69	1
ATCGTGCTTCTTTTTATTATTGTATTTAGCAG	2	202	1
TTCATTAATCTTTTTATAATTTCTTTTTATCG	3	114	1
TTATAATTTCTTTTTATCGTTTCTAGAGGTCT	3	127	1
CTTTAAAGACTTTTTTTGGTATTGCAAAGAGA	4	13	1
    ATCTGATTTTTTTAAATTTTTTATTCTA	5	6	1
TGATTTCTGCTTTTTGTTATCTTCGAGCCACG	5	54	0
TCTTGGGAACTTTTATTCGTTTTATTAAGTAA	5	89	1
          ***** * ****
MAP Score: 11.6402

Motif 4
TGTATACTATCTTGATTGAATTTTTTGTCGACCTAC	0	170	1
GTAAAGAAATCCTTTAAGCATTTTTTAAAAATCAGA	0	208	1
CTGATCAAGACTATTGACTTTTTCCTAGACCGCACT	1	48	0
CGCTAGTTCGCCACTCTAAATTTTTTGATAGGGGTG	1	130	0
TCCTCACTACCTTCTCAAGTCTTTTTCTCTTGAGAA	2	29	1
GTCTTTTTCTCTTGAGAAATTTTTTTTGTTTATTTT	2	47	1
CGAACTGTATCTTCTCTAGATTTTGTTCGATTAGAT	2	148	1
TATCGTGCTTCTTTTTATTATTGTATTTAGCAGACT	2	201	1
TCCGAAAGTTCCTTTAACTTTTCTATTTTT      	3	4	0
TATCCAAACTCCTTTCACCTCTTTAATCTAAAACTT	3	49	0
TTTCATTAATCTTTTTATAATTTCTTTTTATCGTTT	3	113	1
       AGACTTTAAAGACTTTTTTTGGTATTGCA	4	3	1
   AATTCGCCATTTTTGACTTTTATCTCTCTTTGC	4	36	0
  ATCTGATTTTTTTAAATTTTTTATTCTATGGACT	5	8	1
TTCTTGGGAACTTTTATTCGTTTTATTAAGTAAGAT	5	88	1
TACTTGCATTCTTGTCTGCATTTTAAATATAGTACT	6	201	1
          *** * *   **** *
MAP Score: 9.17775

Motif 5
AAAGTTCTTACTCTTCTCTGAAATATAAAATT	0	115	0
GATTTCTTTACTCGTAGGTCGACAAAAAATTC	0	187	0
TTGTTTTTCAATAGTCCCTGGAGCGTAA    	0	282	1
CTAGACCGCACTATCATCTAGAGATAGAGACG	1	28	0
AGACTATTGACTTTTTCCTAGACCGCACTATC	1	45	0
TAGGGGTGAGCTTTTTTCTTAAGTGCCTTCGA	1	106	0
AGAAAGCCTTCCCTTATCTTAAATTCTCGCTA	1	161	0
ATTTCCTAAGCTCTTGGCTTCAAATAAGGACA	1	217	0
TTCTCAAGTCTTTTTCTCTTGAGAAATTTTTT	2	40	1
TGCGAACTGTATCTTCTCTAGATTTTGTTCGA	2	146	1
ATGAGCTTCACTCTCGTCTGAAAATTACAGAG	2	266	0
ATTTCTTTTTATCGTTTCTAGAGGTCTT    	3	132	1
CTACAAAGCCCTCGTGGCTCGAAGATAACAAA	5	42	1
TAAGATTTCCCTAGTCTCTAGAATTATGCGCA	6	98	0
GGTACTTGCATTCTTGTCTGCATTTTAAATAT	6	199	1
       ATAATTTTGCCTACAGCATCTATGG	6	285	0
          ***** *** **
MAP Score: 8.13849

Motif 6
GGAGGTAAGGCTGTGTGTTTGGGGATTTAGATTTGGGATAAAGGA	0	41	1
AGAGTAAGAACTTTATGGACAGTTTTTTGTGATTGCTTGTATACT	0	133	1
TTGTGATTGCTTGTATACTATCTTGATTGAATTTTTTGTCGACCT	0	159	1
CCCTAGAGGGCTTTTTATGAAAAAAGTTGTTTTTCAATAGTCCCT	0	256	1
AAGGTTCAGGCTTCTGATCAAGACTATTGACTTTTTCCTAGACCG	1	52	0
AGGCTTTCTTCTTTCTATGGAATCCTGTATCTTTGTCCTTATTTG	1	184	1
CTTCTCAAGTCTTTTTCTCTTGAGAAATTTTTTTTGTTTATTTTT	2	39	1
TTTTGTTTATTTTTATTATTTAGAACATGATTTTTGGTTTTAATA	2	70	1
ATTTTGCGAACTGTATCTTCTCTAGATTTTGTTCGATTAGATTGA	2	142	1
ATTGACTATTCTTCTTAAATATCGTGCTTCTTTTTATTATTGTAT	2	182	1
ATTGGAATATTTTCATTAATCTTTTTATAATTTCTTTTTATCGTT	3	103	1
   AATTCGCCATTTTTGACTTTTATCTCTCTTTGCAATACCAAA	4	27	0
CAGAAATCAGCTTCTTGGGAACTTTTATTCGTTTTATTAAGTAAG	5	77	1
ATCTTAGTCGTTTTTGAGAGATGCAATTGCATTTTAGTTCTCTTA	6	124	1
GCATTCTTGTCTGCATTTTAAATATAGTACTTTTTAGTGTAGGTC	6	206	1
          **** *           *   ****
MAP Score: 7.36789

Motif 7
GAGTAAGAACTTTATGGACAGTTTTTTGTGATTGCTTGT	0	134	1
GCTTGTATACTATCTTGATTGAATTTTTTGTCGACCTAC	0	167	1
CTCACTACCTTCTCAAGTCTTTTTCTCTTGAGAAATTTT	2	31	1
TTGAGAAATTTTTTTTGTTTATTTTTATTATTTAGAACA	2	58	1
TAGAACATGATTTTTGGTTTTAATATGTTTTGATTGGAC	2	90	1
TCTTCTTAAATATCGTGCTTCTTTTTATTATTGTATTTA	2	191	1
GCTATGGATATTATGAGCTTCACTCTCGTCTGAAAATTA	2	271	0
TTTGGATAAATATTAAGACTAATTCAATTGGAATATTTT	3	77	1
TTAATCTTTTTATAATTTCTTTTTATCGTTTCTAGAGGT	3	118	1
      AGACTTTAAAGACTTTTTTTGGTATTGCAAAGA	4	4	1
ATTCGCCATTTTTGACTTTTATCTCTCTTTGCAATACCA	4	29	0
       ATCTGATTTTTTTAAATTTTTTATTCTATGGA	5	3	1
TGCATTCTTGTCTGCATTTTAAATATAGTACTTTTTAGT	6	205	1
          * *   * ** * * * **
MAP Score: 6.55291

Motif 8
GAGTAAGAACTTTATGGACAGTTTTTTGTGATTGCTTG	0	134	1
TGTATACTATCTTGATTGAATTTTTTGTCGACCTACGA	0	170	1
TCCTCACTACCTTCTCAAGTCTTTTTCTCTTGAGAAAT	2	29	1
GTCTTTTTCTCTTGAGAAATTTTTTTTGTTTATTTTTA	2	47	1
TTTTTATTATTTAGAACATGATTTTTGGTTTTAATATG	2	79	1
TCGTGCTTCTTTTTATTATTGTATTTAGCAGACTATGA	2	203	1
ATTGGAATATTTTCATTAATCTTTTTATAATTTCTTTT	3	103	1
       AGACTTTAAAGACTTTTTTTGGTATTGCAAA	4	3	1
    ATCTGATTTTTTTAAATTTTTTATTCTATGGACT	5	6	1
AAATCAGCTTCTTGGGAACTTTTATTCGTTTTATTAAG	5	80	1
          ***    *   ***** *
MAP Score: 4.98309

Motif 9
GGAGGCTTCTGTTCGTAGAAACAGGAGAGCGAAATTT	0	83	1
TGCCCCTAGAGGGCTTTTTATGAAAAAAGTTGTTTTT	0	253	1
TACGCTCCAGGGACTATTGAAAAACAACTTTTTTCAT	0	272	0
CTAGATGATAGTGCGGTCTAGGAAAAAGTCAATAGTC	1	39	1
TTTTTCTTAAGTGCCTTCGATAAGGAGAAAAGGTTCA	1	89	0
AGATACAGGATTCCATAGAAAGAAGAAAGCCTTCCCT	1	179	0
ACAAAAAAAATTTCTCAAGAGAAAAAGACTTGAGAAG	2	39	0
CAAAAATCATGTTCTAAATAATAAAAATAAACAAAAA	2	69	0
TTATCTCTCTTTGCAATACCAAAAAAAGTCTTTAAAG	4	13	0
GGGCTTTGTAGTCCATAGAATAAAAAATTTAAAAAAA	5	16	0
TTGCATTTTAGTTCTCTTAAAAAAGAGGTTATGTAAT	6	150	1
CCAGAAGGATGGACCTACACTAAAAAGTACTATATTT	6	225	0
          ** *  *  *  *****
MAP Score: 2.93338

Motif 10
GTTCTTACTCTTCTCTGAAATATAAAATTTCGCT	0	110	0
CCTAGAGGGCTTTTTATGAAAAAAGTTGTTTTTC	0	257	1
CCTGAACCTTTTCTCCTTATCGAAGGCACTTAAG	1	87	1
TGAGAAATTTTTTTTGTTTATTTTTATTATTTAG	2	59	1
AGATTGACTATTCTTCTTAAATATCGTGCTTCTT	2	180	1
AATATCGTGCTTCTTTTTATTATTGTATTTAGCA	2	199	1
GAGAGCATAGTTCTCTGTAATTTTCAGACGAGAG	2	254	1
AATTGGAATATTTTCATTAATCTTTTTATAATTT	3	102	1
TTTTTATAATTTCTTTTTATCGTTTCTAGAGGTC	3	124	1
    ATCTGATTTTTTTAAATTTTTTATTCTATG	5	6	1
AGAAATCAGCTTCTTGGGAACTTTTATTCGTTTT	5	78	1
TTGAGAAACGTTCTCGTAAAAGATGGTATTCTAG	5	135	1
TGCATTTTAGTTCTCTTAAAAAAGAGGTTATGTA	6	151	1
          ***** * **  **
MAP Score: 2.81965