AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons011_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237732
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ychF	300	GTP Binding Protein
#1	CPn0334	220	CT079 similarity
#2	pepA	24	Leucyl Aminopeptidase A
#3	ssb	170	SS DNA Binding Protein
#4	CPn0387	132	CT043 hypothetical protein
#5	phnP	221	Metal Dependent Hydrolase
#6	CPn0480	32	CT383 hypothetical protein
#7	artJ	98	Arginine Periplasmic Binding Protein
#8	yhbZ	100	GTP binding protein
#9	rl27	24	L27 ribosomal protein
#10	rl21	300	L21 Ribosomal Protein
#11	trxA	300	Thioredoxin
#12	ctc	300	General Stress Protein

Motif 1
        CGTTTTGTTCTTAGTAAGATTAT	0	2	1
TTTTTTCTACTATTCTTCTTTATCTCTAAGA	0	40	0
TTTTCGTTATTGTTCTTTTTTTCTACTATTC	0	56	0
CATGTCATTATTTTTATTTTTAGATGTCTT 	0	280	1
TTTTTTGTTTTTGTATTTTTT          	1	0	0
ATTAAGTTGATTTTTTTGTTTTTGTATTTTT	1	11	0
TTATATAATATTTTATTTTTAGATTAAAATT	1	80	0
TTAGCTTGATTTTTTATGTTTATCTAAACTG	1	126	0
AGCCTTTAGATTTCTATTTTTAATACTTCTT	3	144	0
ACAAGGGAGTTTTTGATTTTAAGCCTCTGAA	4	42	1
TGTAATAGATTGTTGTTGTTTCAAGTTACCA	4	98	0
ACTGACTAATTATTTTTGTTTGCTTGTGTTT	5	183	1
GAGTTTGATGTATTTATTTTTTTATGTAAAC	7	35	1
  TTCCTATTTTTCGATTTTTCAGAAACATT	8	8	1
AACCGAGCTTTTTTAATGTTTCTGAAAAATC	8	22	0
CAAATCGAGCTTTTTTTGTTTGAAGAAGGAT	8	67	1
AAAAATCTGCTGTTTTTCTTTAAAAAGTTTC	11	105	1
AGTTTCTTAATTGTGTTTTTTATTATCTATA	11	130	1
TTACTGTCCCTGTTATTTTCTTGCAGCTAAG	11	254	0
        AATGTTGTTTTCTCCGTAATCTT	12	287	0
          **** ******
MAP Score: 17.3983

Motif 2
TAAATGAATCTTAGAGATAAAGAAGAATAGTAGAA	0	32	1
AGACAACTCTTCTGTTTCAAAAAAGCACAATAGCT	0	227	0
GTTGTCTTTCTAATATTCGAAAAAGCATGTCATTA	0	255	1
AATAAACTAATTTTAATCTAAAAATAAAATATTAT	1	72	1
ATAAAGTCATTTCTTCTCTAAGAAGAGCTTTATCA	3	52	0
TCTTAAGATGTATTAATTAAAGAAGTATTAAAAAT	3	125	1
TACTTGGAAACTATGGTTTAAAAAGCTATAGAGGA	5	96	1
AACTTTGGATCTTAAAGTCAAGAAGTTGCTAGAAC	5	143	0
     GTGAATTTGTATCAAAGAAGGAACAAGATT	6	5	1
AATAAATACATCAAACTCGAAAAAGTTTTAACTTT	7	18	0
TGTGTTAAAGTTTACATAAAAAAATAAATACATCA	7	40	0
ATCGAGCTTTTTTTGTTTGAAGAAGGATAAAAACG	8	70	1
         CCTTAATAGCAAAAAGAGAGGCGAAG	10	1	1
ATTGAAAGATTCATAAGGAAAAAATTG        	10	283	1
AAATCTGCTGTTTTTCTTTAAAAAGTTTCTTAATT	11	107	1
CTGTTATTTTCTTGCAGCTAAGAAGACTTGAACTT	11	241	0
    AAGTTTCCCTTCTCGAAAAATCGAATTACTG	11	279	0
TTTAGTTGTCTCTTCTTACAAGAAGGATATACGTT	12	91	1
TCAATACTTTCCCTAATTAAAGAATTGAACGTATA	12	118	0
AATTATATCTCCAGTTTGGAAAAAGTCAATACTTT	12	143	0
          ** *  *  ******
MAP Score: 12.848

Motif 3
TGAATCTTAGAGATAAAGAAGAATAGTAGAAAAAA	0	36	1
AGAATAGTAGAAAAAAAGAACAATAACGAAAAGTT	0	55	1
TGAAAATGATAAAAAACCACTATAATCGATTGAAG	0	159	0
AGACATCTAAAAATAAAAATAATGACATGCTTTTT	0	274	0
         AAAAAATACAAAAACAAAAAAATCAA	1	1	1
TACAAAAACAAAAAAATCAACTTAATAAACTAATT	1	16	1
ATTTTAATTAAAAAACTTATTAAGAATAAACTAAT	1	48	1
ATTTTAATCTAAAAATAAAATATTATATAAATAAT	1	81	1
AACTGCTTTTAAACAATTATTTATATAATATTTTA	1	96	0
AAAGCAGTTTAGATAAACATAAAAAATCAAGCTAA	1	122	1
TCAATCTTTTAAATTAGAAAAAAGATGTAGTACTT	3	20	0
TTCTAATTTAAAAGATTGATAAAGCTCTTCTTAGA	3	36	1
TGTATTAATTAAAGAAGTATTAAAAATAGAAATCT	3	133	1
CAGCGCAGTAAAAGATTCATGAGAAAATGTGAGAA	5	27	0
AAACACAAGCAAACAAAAATAATTAGTCAGTCTCT	5	179	0
AATTTGTATCAAAGAAGGAACAAGATTGC      	6	13	1
AAGTTTACATAAAAAAATAAATACATCAAACTCGA	7	33	0
AATGTTTCTGAAAAATCGAAAAATAGGAA      	8	4	0
GATTTTTCAGAAACATTAAAAAAGCTCGGTTTTTT	8	22	1
TTTTTTGTTTGAAGAAGGATAAAAACGTAATC   	8	78	1
TGTAGACTATAGATAATAAAAAACACAATTAAGAA	11	133	0
          *** **  ** ** *
MAP Score: 12.4525

Motif 4
TTAGAGATAAAGAAGAATAGTAGAAAAAAAGA	0	42	1
GAAGAATAGTAGAAAAAAAGAACAATAACGAA	0	53	1
CACAATAGCTAGAAAAATAGTACCTTCAAAAT	0	205	0
TTTTTGAAACAGAAGAGTTGTCTTTCTAATAT	0	239	1
CTCTTCTTAGAGAAGAAATGACTTTATTGACT	3	60	1
TCTGAAAAATCGAAAAATAGGAA         	8	1	0
AACTTTTTAAAGAAAAACAGCAGATTTTTTTG	11	102	0
CTTGCAGCTAAGAAGACTTGAACTTCCATGAG	11	234	0
TTTCCCTTCTCGAAAAATCGAATTACTGTCCC	11	275	0
TACCAAAAGGAGAAGAAAAGGACTCTGGGGTG	12	50	0
          ******** * *
MAP Score: 9.07448

Motif 5
   CGTTTTGTTCTTAGTAAGATTATAAATGAAT	0	7	1
AATTAGTTTATTCTTAATAAGTTTTTTAATTAAA	1	50	0
TTCTCACATTTTCTCATGAATCTTTTACTGCGCT	5	27	1
  CAATTTTTTCCTTATGAATCTTTCAATGCTTA	10	278	0
CAAGTATCTATCCTTAAAAATTTTCGAGAGGGAT	5	68	0
TCTGCTGTTTTTCTTTAAAAAGTTTCTTAATTGT	11	110	1
 AATGTTGTTTTCTCCGTAATCTTGAGCTAAAAG	12	277	0
CAGAAGAGTTGTCTTTCTAATATTCGAAAAAGCA	0	248	1
ATTTTTCGATTTTTCAGAAACATTAAAAAAGCTC	8	15	1
TCTAAGAAGAGCTTTATCAATCTTTTAAATTAGA	3	37	0
          ******  **  **
MAP Score: 3.41647

Motif 6
TTTTCTCATGAATCTTTTACTGCGCTGCAC	5	35	1
TTCAAAGTTAAAACTTTTTCGAGTTTGATG	7	15	1
AAGCCTCTGAAATCGTTTACTAACAAATCA	4	62	1
GAGCTTTATCAATCTTTTAAATTAGAAAAA	3	33	0
        GCAATCTTGTTCCTTCTTTGAT	6	20	0
CACAATTAAGAAACTTTTTAAAGAAAAACA	11	115	0
TTTTTTATGTAAACTTTAACACATGATAGA	7	52	1
AAACAACAACAATCTATTACAAGGAGATTC	4	108	1
TTTCCTTATGAATCTTTCAATGCTTAAAGT	10	274	0
          **********
MAP Score: 1.72942

Motif 7
TGAAGGTACTATTTTTCTAGCTATTGTGCT	0	209	1
AGCTATTGTGCTTTTTTGAAACAGAAGAGT	0	227	1
TAATGACATGCTTTTTCGAATATTAGAAAG	0	260	0
CATTATTTTTATTTTTAGATGTCTT     	0	285	1
ATTCTTAATAAGTTTTTTAATTAAAATTAG	1	45	0
ATAATATTTTATTTTTAGATTAAAATTAGT	1	77	0
GATAGCCTTTAGATTTCTATTTTTAATACT	3	148	0
AATACAAGGGAGTTTTTGATTTTAAGCCTC	4	39	1
TATCCTTAAAAATTTTCGAGAGGGATCTCG	5	64	0
AAAGTTAAAACTTTTTCGAGTTTGATGTAT	7	18	1
TGATGTATTTATTTTTTTATGTAAACTTTA	7	40	1
       GAAAGTTTGCGCTCTATACGCTA	7	85	0
     TTCCTATTTTTCGATTTTTCAGAAA	8	5	1
AATATCAATGAGATTTCGAATTCTTCGCCT	10	28	0
ATAGTCTACAATTTTACGAAACGCAGCTAT	11	158	1
CAGTAATTCGATTTTTCGAGAAGGGAAACT	11	279	1
       AGCGGTTTTTGGTACCGTGCATC	12	3	1
AAAGTATTGACTTTTTCCAAACTGGAGATA	12	143	1
GTCTATCGACAGTTTTCGAGGCAAAATTAT	12	172	0
          **********
MAP Score: 0.300864