AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons026_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238291
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	gcpE	300	GcpE Protein
#1	CPn0533	255	CT406 hypothetical protein
#2	dksA	24	DnaK Suppressor
#3	sfhB	286	predicted Pseudouridine Synthase
#4	cafE	300	Axial Filament Protein

Motif 1
CGAATCGTCCTCTAAAGCAAAATCTTTATCCCCTTGA	0	45	1
GAAATACTTCTCTAAAGAAACGGCTTTAGGGATTCGT	1	118	0
GGTAAAAAATTCTACAGAAATGGCTTTTTGATTCTTT	4	141	0
AGTTTCGACGTCTAGAAACCACTCTTTTCCCAAACAG	4	231	1
ACCTTTACTACCTAGAACCAAGGCTTTTTGAGGATTA	4	16	1
     TGAAATCTTGATAACTTTCTTTACTAGTTTAA	3	264	0
TTTCCTTGTGCCTATACCATATCCTTGAGCTTACTTA	4	270	0
TGTCTAAGATTCAAAAAGAGACTCTTTCTTTCAATAA	3	199	1
CGCATCTTTCCCTTGACTAAAAATTTTGCTTGTCAAA	3	32	1
CCCTTGATTTCCTAGAAAAAAACTTTGCAACTATAGT	1	160	1
CAACAGAATCTTTACAACAAAAGCTTTCCTAGAGTAG	1	24	1
GAACTTCACCTCAATAAGAGGAATTTTCAGAGAGAAA	0	169	0
TTTATCCTGATCTAAAAATTCGGTTTTTCTTAGACTA	1	205	1
GTCTTTGTTTTCTATAATCATTGTCTTTGGTAAGCTA	4	59	0
CAGCATTTTATCTTAATTCAACGCATTTCTATCTTTT	3	128	1
TCTAAGGATGCCTACATTTATCAATTTTACAGAACTT	0	200	0
          **** *  *    ****
MAP Score: 15.6805

Motif 2
ACGAATCGTCCTCTAAAGCAAAATCTTTATC	0	44	1
AAAGCTTTTGTTGTAAAGATTCTGTTGTTAA	1	20	0
TACTCTACTCTAGGAAAGCTTTTGTTGTAAA	1	34	0
CAAAGCAATTTTGCACAGAAATTTAAGATAA	1	86	1
GGAAATACTTCTCTAAAGAAACGGCTTTAGG	1	125	0
GAGACTATAGTTGCAAAGTTTTTTTCTAGGA	1	169	0
GCGAGTGTCTTTGTAAAGCAATTTT      	3	4	0
CGATGGCAGTTTGACAAGCAAAATTTTTAGT	3	47	0
TTTAATGAGTCTAAAAAGATAGAAATGCGTT	3	147	0
GATATTAAACTAGTAAAGAAAGTTATCAAGA	3	260	1
GTAAAGAAAGTTATCAAGATTTCA       	3	272	1
TTTTTGAGGATTAGAAAGATAGCTTACCAAA	4	40	1
AGACCTACAGTTGAAAAGAATTAAATTAAAA	4	92	1
CTAATTATTTTTAAAAAGAATCAAAAAGCCA	4	127	1
AGGTAAAAAATTCTACAGAAATGGCTTTTTG	4	148	0
ACGTTGGTGATTATAAAGAAAATAGGTAAAA	4	171	0
          *** *******
MAP Score: 14.1674

Motif 3
AAAATAATTATTTCATACTTATCAAGGGGATAAAG	0	68	0
AAATAATTATTTTAATTCACAATAATCTCTCCATA	0	90	1
TTCTCTCGGCTTTTATAATTGATAAAACTCTGAAA	0	261	1
GTAGAGTATGTTTTTTTCGTCTCAATAAGCAAAGC	1	57	1
AGTTGCAAAGTTTTTTTCTAGGAAATCAAGGGTAG	1	157	0
     TTGAATTTTATAAGGAGCAAGGTT      	2	5	1
CAAGCAAAATTTTTAGTCAAGGGAAAGATGCGAGT	3	29	0
ATTTCTATCTTTTTAGACTCATTAAATTATTTTTG	3	152	1
AAAGAGACTCTTTCTTTCAATAAAATCGCTAGATC	3	213	1
GTTATTTTAATTTAATTCTTTTCAACTGTAGGTCT	4	92	0
GAAATGGCTTTTTGATTCTTTTTAAAAATAATTAG	4	127	0
          *** *****    **
MAP Score: 9.38782

Motif 4
TATTTTAATTCACAATAATCTCTCCATATACTC	0	97	1
TATCAGCTTCAACAAAATTCTCTCGGCTTTTAT	0	244	1
AAAACTTTGCAACTATAGTCTCTTATATTTATC	1	178	1
CCCCATTTAACAACAGAATCTTTACAACAAAAG	1	14	1
TAAGATTCAAAAAGAGACTCTTTCTTTCAATAA	3	203	1
CTCTTTCTTTCAATAAAATCGCTAGATCCTTAA	3	220	1
AATAATCTCTCCATATACTCTCTTGATGGCCTG	0	110	1
AGAATCTTTACAACAAAAGCTTTCCTAGAGTAG	1	28	1
TTGAGACGAAAAAAACATACTCTACTCTAGGAA	1	49	0
TCGTCCTCTAAAGCAAAATCTTTATCCCCTTGA	0	49	1
ATTGCTTTACAAAGACACTCGCATCTTTCCCTT	3	13	1
          *** * * *****
MAP Score: 9.10479

Motif 5
TCTACGAACACAAAAACAGATTCGAGTTCCTTACG	0	12	1
GAATCGTCCTCTAAAGCAAAATCTTTATCCCCTTG	0	46	1
CCACCCCATTTAACAACAGAATCTTTACAACAAAA	1	11	1
AACAGAATCTTTACAACAAAAGCTTTCCTAGAGTA	1	25	1
ATTGAGACGAAAAAAACATACTCTACTCTAGGAAA	1	48	0
ATACGAATCCCTAAAGCCGTTTCTTTAGAGAAGTA	1	116	1
AGATCAGGATAAATATAAGAGACTATAGTTGCAAA	1	183	0
GTCTAAGATTCAAAAAGAGACTCTTTCTTTCAATA	3	200	1
AATAAAATCGCTAGATCCTTAACTGATTCGATATT	3	231	1
         ACTAAAACCTTTACTACCTAGAACCA	4	1	1
CCTTTACTACCTAGAACCAAGGCTTTTTGAGGATT	4	17	1
AAAAAGAATCAAAAAGCCATTTCTGTAGAATTTTT	4	139	1
GTTTCGACGTCTAGAAACCACTCTTTTCCCAAACA	4	232	1
TTCCTTGTGCCTATACCATATCCTTGAGCTTACTT	4	271	0
          *** * ** *  ***
MAP Score: 9.05833

Motif 6
ATTATTTTAATTCACAATAATCTCTCCATATA	0	95	1
TGAGGTGAAGTTCTGTAAAATTGATAAATGTA	0	193	1
CTTTATCAGCTTCAACAAAATTCTCTCGGCTT	0	241	1
      AAAAATCTCAAAAATTTCAGAGTTTT	0	284	0
TGCACAGAAATTTAAGATAATACGAATCCCTA	1	97	1
CAAAGTTTTTTTCTAGGAAATCAAGGGTAGAG	1	155	0
CACTTAGAATTTTTCAAAAATAATTTAATGAG	3	169	0
GACTCTTTCTTTCAATAAAATCGCTAGATCCT	3	218	1
TAGGTCTTTGTTTTCTATAATCATTGTCTTTG	4	67	0
TTTTTGATTCTTTTTAAAAATAATTAGGTTAT	4	122	0
AAAAAGCCATTTCTGTAGAATTTTTTACCTAT	4	149	1
TTTACCTATTTTCTTTATAATCACCAACGTAA	4	172	1
          ****  ******
MAP Score: 8.38726

Motif 7
ACGAATCGTCCTCTAAAGCAAAATCTTTATCCCC	0	44	1
 CCCACCCCATTTAACAACAGAATCTTTACAACA	1	9	1
  AAAATTGCTTTACAAAGACACTCGCATCTTTC	3	8	1
CGATGGCAGTTTGACAAGCAAAATTTTTAGTCAA	3	44	0
CACTTAGAATTTTTCAAAAATAATTTAATGAGTC	3	167	0
GTGTCTAAGATTCAAAAAGAGACTCTTTCTTTCA	3	198	1
CGATATTAAACTAGTAAAGAAAGTTATCAAGATT	3	259	1
GAAAGATAGCTTACCAAAGACAATGATTATAGAA	4	53	1
TTTTTGATTCTTTTTAAAAATAATTAGGTTATTT	4	120	0
TACGTTGGTGATTATAAAGAAAATAGGTAAAAAA	4	169	0
AACCACTCTTTTCCCAAACAGAATAAGTAAGCTC	4	247	1
          **   ***** ***
MAP Score: 8.34739

Motif 8
TATCAAGGGGATAAAGATTTTGCTTTAGAGGAC	0	51	0
AGGCATCCTTAGAGAAGCTTTATCAGCTTCAAC	0	224	1
CCATTTAACAACAGAATCTTTACAACAAAAGCT	1	16	1
AATCTTTACAACAAAAGCTTTCCTAGAGTAGAG	1	30	1
CTCAATAAGCAAAGCAATTTTGCACAGAAATTT	1	77	1
ATACGAATCCCTAAAGCCGTTTCTTTAGAGAAG	1	116	1
CCGTTTCTTTAGAGAAGTATTTCCTCTACCCTT	1	132	1
GATTTCCTAGAAAAAAACTTTGCAACTATAGTC	1	165	1
TACAAAGACACTCGCATCTTTCCCTTGACTAAA	3	20	1
TTTCCCTTGACTAAAAATTTTGCTTGTCAAACT	3	38	1
TTATTGAAAGAAAGAGTCTCTTTTTGAATCTTA	3	203	0
         ACTAAAACCTTTACTACCTAGAAC	4	1	1
ACTACCTAGAACCAAGGCTTTTTGAGGATTAGA	4	22	1
AAAAAGAATCAAAAAGCCATTTCTGTAGAATTT	4	139	1
          * **** **** *
MAP Score: 8.0206

Motif 9
ATCGTCCTCTAAAGCAAAATCTTTATCCCCTTGAT	0	48	1
ATTGTGAATTAAAATAATTATTTCATACTTATCAA	0	78	0
ATTGAGACGAAAAAAACATACTCTACTCTAGGAAA	1	48	0
CTCAATAAGCAAAGCAATTTTGCACAGAAATTTAA	1	77	1
GATTTCCTAGAAAAAAACTTTGCAACTATAGTCTC	1	165	1
GAATTTTTCAAAAATAATTTAATGAGTCTAAAAAG	3	160	0
TTAAACTAGTAAAGAAAGTTATCAAGATTTCA   	3	264	1
CCTACAGTTGAAAAGAATTAAATTAAAATAACCTA	4	95	1
ATTCTTTTTAAAAATAATTAGGTTATTTTAATTTA	4	113	0
TGGTGATTATAAAGAAAATAGGTAAAAAATTCTAC	4	163	0
TTTCCCAAACAGAATAAGTAAGCTCAAGGATATGG	4	256	1
          **** ** **  * *
MAP Score: 5.72963

Motif 10
GAACACAAAAACAGATTCGAGTTCCTTACGAA	0	17	1
TCAAGGGGATAAAGATTTTGCTTTAGAGGACG	0	50	0
TTGTGAATTAAAATAATTATTTCATACTTATC	0	80	0
ATAAAAGCCGAGAGAATTTTGTTGAAGCTGAT	0	245	0
 AAAAATCTCAAAAATTTCAGAGTTTTATCAA	0	279	0
CTTTTGTTGTAAAGATTCTGTTGTTAAATGGG	1	15	0
CTACTCTAGGAAAGCTTTTGTTGTAAAGATTC	1	29	0
AATTTTGCACAGAAATTTAAGATAATACGAAT	1	92	1
ATACTTCTCTAAAGAAACGGCTTTAGGGATTC	1	120	0
ATCCTGATCTAAAAATTCGGTTTTTCTTAGAC	1	208	1
TCCCTTGACTAAAAATTTTGCTTGTCAAACTG	3	40	1
AATTTTTCAAAAATAATTTAATGAGTCTAAAA	3	162	0
ATTATTTTTGAAAAATTCTAAGTGTCTAAGAT	3	177	1
CTACAGTTGAAAAGAATTAAATTAAAATAACC	4	96	1
TTCTTTTTAAAAATAATTAGGTTATTTTAATT	4	115	0
TTATTTTTAAAAAGAATCAAAAAGCCATTTCT	4	131	1
AAAATAGGTAAAAAATTCTACAGAAATGGCTT	4	152	0
ACGAGCAGTTAGAAATTTAAGTTTCGACGTCT	4	212	1
          ******** * *
MAP Score: 4.48295