AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons027_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238369
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rl13	231	L13 Ribosomal Protein
#1	CPn0249	57	CT151 hypothetical protein
#2	CPn0525	300	CT398 hypothetical protein
#3	CPn0755	260	CT616 hypothetical protein
#4	rpoD	158	RNA Polymerase Sigma-66
#5	dnaG	300	DNA Primase

Motif 1
CAGCAGCCGTTAAGAAAAAACTGCTAATTGTACG	0	88	1
TCTCTTAGTTTAAAAATATTTCCATAAATTTCTT	0	124	0
GACTTCTAACTAAGAATACGATTTTAGAAGCGAG	1	33	0
          TAAAAATTTTCTCAACATTTAAAA	2	0	1
TAGTAAAAAATAAAAATATACTTTTAAATGTTGA	2	21	0
TATTTTTTACTAAAAATGATTAAATGCGCTTTGG	2	43	1
ATTGTTCCTGTAAGAACACTTCCAAAGCGCATTT	2	64	0
AATTTACAAGTAAAAATTATATGAATGGCTAGAC	2	95	1
ACATTAGTTCTAAGAAAAGGGCATTTCGCTTGCT	2	127	1
CTCAAATTTATAAGAATTTTCCTTACAAAAAAAC	2	159	1
TTAAGTTTCCTAAGAAAGCCAAAAATCACTATGG	2	260	0
GTATCGAAAATAAGAAAAAGCTTTCCTTTCTCTC	3	77	0
ATACACATATTAAGAAAAAAGAGAATTTATGAGA	3	107	1
TTATGAGAAATAAAAAAAGTTTTATGCCAACATA	3	133	1
AACATAACAATAAGAATGGTCTTAAAAAAATACT	3	161	1
TCAACAAAAATAAGAATAAATTGCTCTTCATAGC	3	218	0
     GGAGTTAAGAATGCTGCATTACGAGCCGG	5	5	1
TTTCTTTTTATAAGAATTCCCTAATATAAAAGAA	5	129	1
CTTTTTAAACTAAGAAATCTGTAAGTTAAAATTG	5	251	1
          ********   * *
MAP Score: 16.643

Motif 2
TCGTCAGCGTATAAGATAAAAATCCCTAGA	4	67	1
TCCCCTTGAGAAAAGATAAACAGGATGGGA	5	39	1
TCAGCAGCCGTTAAGAAAAAACTGCTAATT	0	87	1
TGTATCGAAAATAAGAAAAAGCTTTCCTTT	3	82	0
GATACACATATTAAGAAAAAAGAGAATTTA	3	106	1
ACTTTAAGATTTAAAATAAACTGCTATTAA	3	32	1
CTGAGGCTCTATAAAATAAAGAGACTCTCC	5	220	0
          AAAAAATAAATCCTTATATC	3	250	0
CATTTTTAGTAAAAAATAAAAATATACTTT	2	31	0
ATTCCCTAATATAAAAGAAATTCATCCAGA	5	144	1
GGAATTCTTATAAAAAGAAATTTTCTATTT	5	119	0
CCCTCTGATTTCAAGATAAATCCATATTTT	0	19	1
GCGATACATGTGAAGAAAAATACAGTTTAC	2	219	0
TGGGATGCTGTAAATAGAAAATTTCTTTTT	5	108	1
AAAAGAGAATTTATGAGAAATAAAAAAAGT	3	123	1
          **********
MAP Score: 15.8428

Motif 3
TCTGATTTCAAGATAAATCCATATTTTTGAGATCTAGC	0	22	1
TTTTAGTAAAAAATAAAAATATACTTTTAAATGTTGAG	2	20	0
TTTAGGCAAGAAGTAAAGCATGTTTTTTTGTAAGGAAA	2	176	0
ATTTTTGTTGATATAAGGATTTATTTTTT         	3	241	1
   GACTTCTAACTAAGAATACGATTTTAGAAGCGAGT	1	32	0
GCCTAAAAAGAGGTAAACTGTATTTTTCTTCACATGTA	2	207	1
TGTGTATCGAAAATAAGAAAAAGCTTTCCTTTCTCTCT	3	76	0
TAGGAAACTTAAGTAAGGAATAATTTTC          	2	282	1
TTTTTATTTCTCATAAATTCTCTTTTTTCTTAATATGT	3	111	0
ATAAGAATGGTCTTAAAAAAATACTTTTCTAATCAAAT	3	170	1
ATCAAATTGTTGGTAAGATATTGATTTTCGTCAGCGTA	4	40	1
TAGGGAATTCTTATAAAAAGAAATTTTCTATTTACAGC	5	114	0
AATTTATGAGAAATAAAAAAAGTTTTATGCCAACATAA	3	130	1
ACGAAAAGAAATTTATGGAAATATTTTTAAACTAAGAG	0	119	1
TAGCAGTTTATTTTAAATCTTAAAGTTCTTGTCTTGTC	3	20	0
          *  ****   *   ****
MAP Score: 15.4701

Motif 4
AAACTGCTAATTGTACGAAAAGAAATTTATGGAAA	0	105	1
ATGGAAATATTTTTAAACTAAGAGACTTGTTATTT	0	133	1
GTTCAAATTTTTTTCCAAACAAAAACAGCCGAAAA	0	165	0
    TAAAAATTTTCTCAACATTTAAAAGTATATT	2	6	1
ATTTAATCATTTTTAGTAAAAAATAAAAATATACT	2	33	0
CGAAATGCCCTTTTCTTAGAACTAATGTCTAGCCA	2	120	0
TTTATAAGAATTTTCCTTACAAAAAAACATGCTTT	2	165	1
TAAACTGTATTTTTCTTCACATGTATCGCATTCCT	2	220	1
CTTTTTCTTATTTTCGATACACATATTAAGAAAAA	3	91	1
ATAAAAAAAGTTTTATGCCAACATAACAATAAGAA	3	142	1
AAAAAAATACTTTTCTAATCAAATAGAACTTATGG	3	184	1
AAATAAATCCTTATATCAACAAAAATAAGAATAAA	3	232	0
ACAACTTTCCTCATAGAAGAAGAAATAGTA     	4	5	0
AATCCCCTTGTTTTATTCCAAGTAAGAAAG     	4	138	1
ATTAGGGAATTCTTATAAAAAGAAATTTTCTATTT	5	119	0
TAAAAGAAATTCATCCAGAAAGAAAAGCTGCATTA	5	155	1
GCCTCAGTCTTTTTAAACTAAGAAATCTGTAAGTT	5	243	1
          *****    ** ***
MAP Score: 14.7265

Motif 5
AAAAAACTGCTAATTGTACGAAAAGAAATTTATGGAAATA	0	102	1
TTTTCGGCTGTTTTTGTTTGGAAAAAAATTTGAACAGACT	0	165	1
AATATACTTTTAAATGTTGAGAAAATTTTTA         	2	1	0
TATATTTTTATTTTTTACTAAAAATGATTAAATGCGCTTT	2	35	1
AAAAATTATATGAATGGCTAGACATTAGTTCTAAGAAAAG	2	106	1
AAAGCATGTTTTTTTGTAAGGAAAATTCTTATAAATTTGA	2	160	0
CATGCTTTACTTCTTGCCTAAAAAGAGGTAAACTGTATTT	2	192	1
AAGCTTTTTCTTATTTTCGATACACATATTAAGAAAAAAG	3	88	1
TAAAAAAAGTTTTATGCCAACATAACAATAAGAATGGTCT	3	143	1
CCATAAGTTCTATTTGATTAGAAAAGTATTTTTTTAAGAC	3	179	0
TTTATTCTTATTTTTGTTGATATAAGGATTTATTTTTT  	3	232	1
TTGTATCAAATTGTTGGTAAGATATTGATTTTCGTCAGCG	4	36	1
TATTAGGGAATTCTTATAAAAAGAAATTTTCTATTTACAG	5	115	0
GGTAAATTAATAATTGGGGAGAGTCTCTTTATTTTATAGA	5	203	1
          ** ***   * * *    **
MAP Score: 13.6546

Motif 6
CTCTGATTTCAAGATAAATCCATATTTTTGAGA	0	21	1
TAATTGTACGAAAAGAAATTTATGGAAATATTT	0	112	1
CCTCTCTAGTAAGACAGTTACATTATT      	0	214	1
TTTTTAGTAAAAAATAAAAATATACTTTTAAAT	2	26	0
CATTAGTTCTAAGAAAAGGGCATTTCGCTTGCT	2	128	1
GTTTTTTTGTAAGGAAAATTCTTATAAATTTGA	2	160	0
TTTCCTTACAAAAAAACATGCTTTACTTCTTGC	2	176	1
GATACATGTGAAGAAAAATACAGTTTACCTCTT	2	214	0
         GAAAATTATTCCTTACTTAAGTTT	2	286	0
ATCTCCAGACAAGACAAGAACTTTAAGATTTAA	3	13	1
TGAGAGAGAAAGGAAAGCTTTTTCTTATTTTCG	3	74	1
ATGAGAAATAAAAAAAGTTTTATGCCAACATAA	3	135	1
AGAATGGTCTTAAAAAAATACTTTTCTAATCAA	3	173	1
        AAAAAATAAATCCTTATATCAACAA	3	245	0
TTCTTCTATGAGGAAAGTTGTATCAAATTGTTG	4	19	1
    GGAGTTAAGAATGCTGCATTACGAGCCGG	5	6	1
ATGCTGTAAATAGAAAATTTCTTTTTATAAGAA	5	112	1
TCCCTAATATAAAAGAAATTCATCCAGAAAGAA	5	146	1
TCATCCAGAAAGAAAAGCTGCATTAGACAAAAT	5	165	1
TCTGTAAGTTAAAATTGCAGCATAACCAAGTTG	5	268	1
          **** ** * ***
MAP Score: 13.1533

Motif 7
TTCGGCTGTTTTTGTTTGGAAAAAAATTTGAACAGACTT	0	167	1
TTTAATCATTTTTAGTAAAAAATAAAAATATACTTTTAA	2	28	0
TTATAAGAATTTTCCTTACAAAAAAACATGCTTTACTTC	2	166	1
AAAAAATACTTTTCTAATCAAATAGAACTTATGGCTATG	3	185	1
TATTAGGGAATTCTTATAAAAAGAAATTTTCTATTTACA	5	116	0
CATGCTTTACTTCTTGCCTAAAAAGAGGTAAACTGTATT	2	192	1
AGCCTCAGTCTTTTTAAACTAAGAAATCTGTAAGTTAAA	5	242	1
TATGGAAATATTTTTAAACTAAGAGACTTGTTATTTTCG	0	132	1
AAAACTGCTAATTGTACGAAAAGAAATTTATGGAAATAT	0	104	1
ATAAAAGAAATTCATCCAGAAAGAAAAGCTGCATTAGAC	5	154	1
CGATACACATATTAAGAAAAAAGAGAATTTATGAGAAAT	3	105	1
AAAGAGAATTTATGAGAAATAAAAAAAGTTTTATGCCAA	3	124	1
TAACAATAAGAATGGTCTTAAAAAAATACTTTTCTAATC	3	165	1
AAAATATACTTTTAAATGTTGAGAAAATTTTTA      	2	4	0
          ***      *** ***  *
MAP Score: 11.1272

Motif 8
TCAAAAATATGGATTTATCTTGAAATCAGAG	0	21	0
AGACGGTGTCTGAATGCTTTTATATCAGCAG	0	63	1
ATATTTCCATAAATTTCTTTTCGTACAATTA	0	112	0
GAAATTTATGGAAATATTTTTAAACTAAGAG	0	126	1
TAAGTCTGTTCAAATTTTTTTCCAAACAAAA	0	176	0
TCAACATTTAAAAGTATATTTTTATTTTTTA	2	21	1
ATGCGCTTTGGAAGTGTTCTTACAGGAACAA	2	66	1
TTTTGTAAGGAAAATTCTTATAAATTTGAGC	2	158	0
CAAGAAGTAAAGCATGTTTTTTTGTAAGGAA	2	177	0
TTTAAATCTTAAAGTTCTTGTCTTGTCTGGA	3	16	0
GATTTAAAATAAACTGCTATTAATTGCAGAT	3	39	1
TGTTGGCATAAAACTTTTTTTATTTCTCATA	3	134	0
TTTGATTAGAAAAGTATTTTTTTAAGACCAT	3	176	0
AAATAAGAATAAATTGCTCTTCATAGCCATA	3	214	0
GTTGATATAAGGATTTATTTTTT        	3	247	1
TGTTGGTAAGATATTGATTTTCGTCAGCGTA	4	47	1
TGTAAATAGAAAATTTCTTTTTATAAGAATT	5	116	1
TTTATATTAGGGAATTCTTATAAAAAGAAAT	5	128	0
CTTTCTGGATGAATTTCTTTTATATTAGGGA	5	146	0
          *** *******
MAP Score: 2.40704