AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons027_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238349
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rl13	231	L13 Ribosomal Protein
#1	CPn0525	300	CT398 hypothetical protein
#2	rpoD	158	RNA Polymerase Sigma-66
#3	dnaG	300	DNA Primase

Motif 1
GAAAACACTCCCTCTGATTTCAAGATAAATCCATATT	0	10	1
ACGAGCCGGTCCCCTTGAGAAAAGATAAACAGGATGG	3	30	1
GCTTTTATATCAGCAGCCGTTAAGAAAAAACTGCTAA	0	78	1
TATAAGAATTCCCTAATATAAAAGAAATTCATCCAGA	3	137	1
TTTAGGAATGCGATACATGTGAAGAAAAATACAGTTT	1	221	0
GAGCCTCAGTCTTTTTAAACTAAGAAATCTGTAAGTT	3	241	1
TATTGATTTTCGTCAGCGTATAAGATAAAAATCCCTA	2	58	1
ATACAACTTTCCTCATAGAAGAAGAAATAGTA     	2	5	0
GAATGGCTAGACATTAGTTCTAAGAAAAGGGCATTTC	1	117	1
ATATTAGGGAATTCTTATAAAAAGAAATTTTCTATTT	3	119	0
AAGTTGTATCAAATTGTTGGTAAGATATTGATTTTCG	2	33	1
TAAGAAAAAACTGCTAATTGTACGAAAAGAAATTTAT	0	98	1
AATAACAAGTCTCTTAGTTTAAAAATATTTCCATAAA	0	130	0
CCTTAGAGGACAGTTTAGTCAAAGGAAGATAGGAAAT	2	96	0
GAAAGAAAAGCTGCATTAGACAAAATACAGAGGTAAA	3	172	1
ATTTATAAGAATTTTCCTTACAAAAAAACATGCTTTA	1	164	1
GCATTTAATCATTTTTAGTAAAAAATAAAAATATACT	1	33	0
TCCCCTTGTTTTATTCCAAGTAAGAAAG         	2	140	1
TTTTCGGCTGTTTTTGTTTGGAAAAAAATTTGAACAG	0	165	1
          *  **   *  ******
MAP Score: 16.9477

Motif 2
GCCGTTAAGAAAAAACTGCTAATTGTACGA	0	93	1
AATTGTACGAAAAGAAATTTATGGAAATAT	0	113	1
TTTTCCAAACAAAAACAGCCGAAAATAACA	0	160	0
TTTTGTTTGGAAAAAAATTTGAACAGACTT	0	176	1
CCCTCTCTAGTAAGACAGTTACATTATT  	0	213	1
          TAAAAATTTTCTCAACATTT	1	0	1
CTCAAATTTATAAGAATTTTCCTTACAAAA	1	159	1
TTAAGTTTCCTAAGAAAGCCAAAAATCACT	1	264	0
CTTCTTCTATGAGGAAAGTTGTATCAAATT	2	18	1
CAAAGGAAGATAGGAAATCTAGGGATTTTT	2	84	0
TCTAGCCTTAGAGGACAGTTTAGTCAAAGG	2	108	0
     GGAGTTAAGAATGCTGCATTACGAG	3	5	1
ATTCTTATAAAAAGAAATTTTCTATTTACA	3	116	0
TTTCTTTTTATAAGAATTCCCTAATATAAA	3	129	1
CCCTAATATAAAAGAAATTCATCCAGAAAG	3	147	1
TTCATCCAGAAAGAAAAGCTGCATTAGACA	3	164	1
CTTTTTAAACTAAGAAATCTGTAAGTTAAA	3	251	1
          **********
MAP Score: 14.5918

Motif 3
GGTGTCTGAATGCTTTTATATCAGCAGCCGTTAAGAA	0	67	1
AAAAAACTGCTAATTGTACGAAAAGAAATTTATGGAA	0	102	1
TTTATGGAAATATTTTTAAACTAAGAGACTTGTTATT	0	130	1
TTTTCGGCTGTTTTTGTTTGGAAAAAAATTTGAACAG	0	165	1
AAGTATATTTTTATTTTTTACTAAAAATGATTAAATG	1	32	1
GCTTTGGAAGTGTTCTTACAGGAACAATTTACAAGTA	1	70	1
GGCTAGACATTAGTTCTAAGAAAAGGGCATTTCGCTT	1	121	1
TTTATAAGAATTTTCCTTACAAAAAAACATGCTTTAC	1	165	1
AAACATGCTTTACTTCTTGCCTAAAAAGAGGTAAACT	1	189	1
GATACAACTTTCCTCATAGAAGAAGAAATAGTA    	2	6	0
AGAAATCCCCTTGTTTTATTCCAAGTAAGAAAG    	2	135	1
CCCATCCTGTTTATCTTTTCTCAAGGGGACCGGCTCG	3	31	0
TAAATAGAAAATTTCTTTTTATAAGAATTCCCTAATA	3	118	1
CTGGATGAATTTCTTTTATATTAGGGAATTCTTATAA	3	136	0
CTAATGCAGCTTTTCTTTCTGGATGAATTTCTTTTAT	3	154	0
AGAGCCTCAGTCTTTTTAAACTAAGAAATCTGTAAGT	3	240	1
          *  ** **    *****
MAP Score: 12.4588

Motif 4
CGAAAATAACAAGTCTCTTAGTTTAAAAATATTTC	0	136	0
TGTAAATAGAAAATTTCTTTTTATAAGAATTCCCT	3	116	1
  AATAATGTAACTGTCTTACTAGAGAGGGCGATT	0	208	0
TGAGCAAGCGAAATGCCCTTTTCTTAGAACTAATG	1	128	0
CTAAGGCTAGAAATCCCCTTGTTTTATTCCAAGTA	2	127	1
AATTTGATACAACTTTCCTCATAGAAGAAGAAATA	2	13	0
TAATTGGGGAGAGTCTCTTTATTTTATAGAGCCTC	3	213	1
TTTAACTTACAGATTTCTTAGTTTAAAAAGACTGA	3	246	0
ATATTTCCATAAATTTCTTTTCGTACAATTAGCAG	0	108	0
CTTTTTATAAGAATTCCCTAATATAAAAGAAATTC	3	132	1
CAACATTTAAAAGTATATTTTTATTTTTTACTAAA	1	22	1
AAAAGAGGTAAACTGTATTTTTCTTCACATGTATC	1	212	1
TACTACCGAGAATTGCCTTGGAATTAATATCCCAT	3	63	0
          ** * ****  * **
MAP Score: 10.1228

Motif 5
       GAAAACACTCCCTCTGATTTCAAGATAAATCCA	0	3	1
GCCGAAAATAACAAGTCTCTTAGTTTAAAAATATTTCCAT	0	133	0
        TAAAAATTTTCTCAACATTTAAAAGTATATTT	1	2	1
TTGAGCAAGCGAAATGCCCTTTTCTTAGAACTAATGTCTA	1	124	0
TTTTTGTAAGGAAAATTCTTATAAATTTGAGCAAGCGAAA	1	150	0
TAAGAAAGCCAAAAATCACTATGGAGTTTAGGAATGCGAT	1	244	0
          GAAAATTATTCCTTACTTAAGTTTCCTAAG	1	280	0
ACAATTTGATACAACTTTCCTCATAGAAGAAGAAATAGTA	2	10	0
ATACGCTGACGAAAATCAATATCTTACCAACAATTTGATA	2	39	0
CGTATAAGATAAAAATCCCTAGATTTCCTATCTTCCTTTG	2	74	1
ATTTACTACCGAGAATTGCCTTGGAATTAATATCCCATCC	3	61	0
CTTATAAAAAGAAATTTTCTATTTACAGCATCCCAGGGAA	3	103	0
TTCTTTTTATAAGAATTCCCTAATATAAAAGAAATTCATC	3	130	1
TAATATAAAAGAAATTCATCCAGAAAGAAAAGCTGCATTA	3	150	1
AATAATTGGGGAGAGTCTCTTTATTTTATAGAGCCTCAGT	3	211	1
          **** ** **    *    *
MAP Score: 6.58435

Motif 6
TCCCTCTGATTTCAAGATAAATCCATATTTTTGAG	0	18	1
TGCTAATTGTACGAAAAGAAATTTATGGAAATATT	0	109	1
GTCTCTTAGTTTAAAAATATTTCCATAAATTTCTT	0	124	0
AAAACAGCCGAAAATAACAAGTCTCTTAGTTTAAA	0	144	0
CTTTTAAATGTTGAGAAAATTTTTA          	1	0	0
CTCAACATTTAAAAGTATATTTTTATTTTTTACTA	1	20	1
CTTGCTCAAATTTATAAGAATTTTCCTTACAAAAA	1	155	1
TAAAAAGAGGTAAACTGTATTTTTCTTCACATGTA	1	210	1
GAAACTTAAGTAAGGAATAATTTTC          	1	285	1
TTACCAACAATTTGATACAACTTTCCTCATAGAAG	2	21	0
CGTCAGCGTATAAGATAAAAATCCCTAGATTTCCT	2	68	1
TAGTCAAAGGAAGATAGGAAATCTAGGGATTTTTA	2	83	0
ACTGTCCTCTAAGGCTAGAAATCCCCTTGTTTTAT	2	119	1
GGATATTAATTCCAAGGCAATTCTCGGTAGTAAAT	3	66	1
TGGGATGCTGTAAATAGAAAATTTCTTTTTATAAG	3	108	1
AAAATTTCTTTTTATAAGAATTCCCTAATATAAAA	3	125	1
AATTCCCTAATATAAAAGAAATTCATCCAGAAAGA	3	143	1
GCAACTTGGTTATGCTGCAATTTTAACTTACAGAT	3	267	0
          ** *  * ** ****
MAP Score: 6.31372

Motif 7
CTCTGATTTCAAGATAAATCCATATTTTTGAGA	0	21	1
CCTCTCTAGTAAGACAGTTACATTATT      	0	214	1
CATTAGTTCTAAGAAAAGGGCATTTCGCTTGCT	1	128	1
TTTCCTTACAAAAAAACATGCTTTACTTCTTGC	1	176	1
TTCTTCTATGAGGAAAGTTGTATCAAATTGTTG	2	19	1
    GGAGTTAAGAATGCTGCATTACGAGCCGG	3	6	1
TCCCTAATATAAAAGAAATTCATCCAGAAAGAA	3	146	1
TCATCCAGAAAGAAAAGCTGCATTAGACAAAAT	3	165	1
TCTGTAAGTTAAAATTGCAGCATAACCAAGTTG	3	268	1
          **** ** * ***
MAP Score: 1.08091