AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID014_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391001
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rfbA	57	glucose-1-phosphate thymidylyltransferase
#1	rfbB	300	dTDP-glucose 4,6 dehydratase
#2	trxA	76	thioredoxin 1
#3	rhoL	140	rho operon leader peptide
#4	rho	84	transcription termination factor Rho; polarity suppressor
#5	rfe	239	UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA)

Motif 1
       TGTTGCGAATCTTCCTGCCGTTGTTTTATATAAACCA	1	3	1
GCTCTGGAAACAAGGAAAATCCTGGAAAACTTTGAATAAAACCC	1	72	0
TTTACAGCTACCAGAGCACTGCATGCATGCCTATGATGTGACGA	1	173	0
AAAGCCAGGGGCGGTAGCGTGCATTAATACCTCTATTAATCAAA	1	214	1
GGACGCCCGGCGTGAGTCATGCTAACTTAGTGTTGACTTCGTAT	3	47	1
AAGTTTGAATCTTGTAATTTCCAACGCTTCCCGTTTTATCTTAA	3	106	1
CGTAAACAGGCATGGATGATCCTGCCATACCATTCACAACATTA	4	11	1
ACGTGTTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATG	5	33	1
CAGCAAATTCCAGGAATTTTCCTAACATCGCCAGCGCGGCATTA	5	72	0
TAGGAAAATTCCTGGAATTTGCTGGCATGTTATGCAATTTGCAT	5	92	1
          *  * *   ****    *  *  *
MAP Score: 6.80884

Motif 2
TGGTTTATATAAAACAACGGCAGGAAGATTCGCAA	1	12	0
TCGTCACATCATAGGCATGCATGCAGTGCTCTGGT	1	173	1
GCATGCATGCAGTGCTCTGGTAGCTGTAAAGCCAG	1	187	1
TGGTAGCTGTAAAGCCAGGGGCGGTAGCGTGCATT	1	204	1
TTTGATTAATAGAGGTATTAATGCACGCTACCGCC	1	223	0
TTAAGATAAAACGGGAAGCGTTGGAAATTACAAGA	3	115	0
    CCGTAAACAGGCATGGATGATCCTGCCATAC	4	6	1
TAATGTTGTGAATGGTATGGCAGGATCATCCATGC	4	20	0
TTTTCCTAACATCGCCAGCGCGGCATTAAGATTAC	5	65	0
TAATTTTTGCACAGGACTGGTGGGTTTGGAACGGA	5	146	1
CCTTCTGAATAAAGGTCTTCGTGGTTATACTTCTG	5	186	1
          *  ** ****  ***
MAP Score: 4.01934

Motif 3
         TGTTGCGAATCTTCCTGCCGTTGTTTTATAT	1	1	1
TTCACAGCATGCTCTGAAGTAATATGGAATAAATTAA   	1	273	1
 CCGTAAACAGGCATGGATGATCCTGCCATACCATTCACA	4	9	1
AAAGCAAAACGCCACGTAAACACGTGGCGTTTTTGGCATA	5	18	0
CGCTGGCGATGTTAGGAAAATTCCTGGAATTTGCTGGCAT	5	80	1
GGACTGGTGGGTTTGGAACGGACTTTCCCTTCTGAATAAA	5	159	1
          * *  * *    * **** *
MAP Score: 2.46591

Motif 4
TAATTCATCTTGCTCCACCATCACGAACAAGAT	0	20	0
CTTACCAATCCGCTCTGGAAACAAGGAAAATCC	1	94	0
ATGCATGCAGTGCTCTGGTAGCTGTAAAGCCAG	1	189	1
CTTCAGAGCATGCTGTGAAATAAGCGGCTCTCA	1	259	0
TTTCACAGCATGCTCTGAAGTAATATGGAATAA	1	272	1
CGAAAGCGTATCCGGTGAAATAAAGTCAACCTT	2	43	1
GCATGGATGATCCTGCCATACCATTCACAACAT	4	20	1
AACCCACCAGTCCTGTGCAAAAATTAACCATTT	5	139	0
    AATGCATGCTCTCAGAGAAAATTATTAGC	5	220	0
          *******  * **
MAP Score: 2.4418

Motif 5
TCACATCATAGGCATGCATGCAGTGCTCTG	1	176	1
CAGGGGCGGTAGCGTGCATTAATACCTCTA	1	219	1
     CCGTAAACAGGCATGGATGATCCTG	4	5	1
TCCTGGAATTTGCTGGCATGTTATGCAATT	5	101	1
TTTCTCTGAGAGCATGCATT          	5	229	1
          **********
MAP Score: 1.62033

Motif 6
CGTGATGGTGGAGCAAGATGAATTAAAAGGAATGATGAA 	0	28	1
GAAAATCCTGGAAAACTTTGAATAAAACCCTACTGCTAAC	1	62	0
CGTGCATTAATACCTCTATTAATCAAACTGAGAGCCGCTT	1	231	1
TTACTTCAGAGCATGCTGTGAAATAAGCGGCTCTCAGTTT	1	255	0
TTATTTCACAGCATGCTCTGAAGTAATATGGAATAAATTA	1	269	1
TTACGAAAGCGTATCCGGTGAAATAAAGTCAACCTTTAGT	2	40	1
GGAACGGACTTTCCCTTCTGAATAAAGGTCTTCGTGGTTA	5	173	1
          *    ** ****  **   *
MAP Score: 1.07602

Motif 7
GTAACGCTCGTCACATCATAGGCATGCATG	1	166	1
AGCTACCAGAGCACTGCATGCATGCCTATG	1	182	0
GCCGCTTATTTCACAGCATGCTCTGAAGTA	1	264	1
GCCATACCATTCACAACATTAAGTTCGAGA	4	34	1
TATGCAAATTGCATAACATGCCAGCAAATT	5	107	0
          **********
MAP Score: 0.629895

Motif 8
TCACATCATAGGCATGCATGCAGTGCTCTG	1	176	1
CTTATTTCACAGCATGCTCTGAAGTAATAT	1	268	1
 CCGTAAACAGGCATGGATGATCCTGCCAT	4	9	1
GGAATTTGCTGGCATGTTATGCAATTTGCA	5	105	1
TTTCTCTGAGAGCATGCATT          	5	229	1
          **********
MAP Score: 0.240786

Motif 9
TTTTCCTTGTTTCCAGAGCGGATTGGTAAG	1	97	1
CTAATTGTCTTACCAATCCGCTCTGGAAAC	1	105	0
ACCCGAAAAATTCAAACGCTAATTGTCTTA	1	123	0
GCTTTACAGCTACCAGAGCACTGCATGCAT	1	189	0
ACTATTGCTTTACGAAAGCGTATCCGGTGA	2	31	1
ATCTTGTAATTTCCAACGCTTCCCGTTTTA	3	114	1
TTCCTAACATCGCCAGCGCGGCATTAAGAT	5	68	0
GTTCCAAACCCACCAGTCCTGTGCAAAAAT	5	148	0
          **********
MAP Score: 0.0158246