AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID011_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943390971
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	trpE	91	anthranilate synthase component I
#1	trpL	137	trp operon leader peptide
#2	pabB	73	p-aminobenzoate synthetase, component I
#3	pabA	31	p-aminobenzoate synthetase, component II
#4	yhfG	104	orf, hypothetical protein
#5	ppiA	270	peptidyl-prolyl cis-trans isomerase A (rotamase A)

Motif 1
ATCACCTAAAATCGCCCGCTCGCGGCATAT	5	47	0
CGCGGGCAATCTTGCCCGCGCTTCTGCTCT	4	20	1
CGCGGGCAAGATTGCCCGCGCGAGAAATCA	4	10	0
CGCTCGCGGCATATCCCGCTATGCCATTTT	5	31	0
AATCAGATACCCAGCCCGCCTAATGAGCGG	0	40	1
TGTTCAAAAAAAAGCCCGCTCATTAGGCGG	0	55	0
CGCGCTTCTGCTCTCCCGGCGTAACCCGGA	4	36	1
         AATAGCGCGGTTCTTTTGTAC	3	1	1
TGGTGAATACACTGCCCGTT          	0	0	0
      GGCGCACTCCCGTTCTGGATAATG	1	4	1
CGTAACCCGGATTTGCCGCTTATACTTGTG	4	55	1
      TGTTAACTCCTGCTAAATTGTTGG	2	4	1
          **********
MAP Score: 15.4015

Motif 2
        AACGGGCAGTGTATTCACCATGCGTA	0	2	1
GCTCATTAGGCGGGCTGGGTATCTGATTGCTTTA	0	34	0
GCCCGCCTAATGAGCGGGCTTTTTTTTGAACAAA	0	53	1
TGAAATAATTAGCGCCAACAATTTAGCAGGAGTT	2	14	0
       AATAGCGCGGTTCTTTTGTACCGGAGC	3	3	1
  TGATTTCTCGCGCGGGCAATCTTGCCCGCGCT	4	8	1
CGGCATATCCCGCTATGCCATTTTATTTTTGAAC	5	21	0
GGATATGCCGCGAGCGGGCGATTTTAGGTGATTT	5	45	1
AATTAGGTAAAGGGATGGCCTTGTTCTTGAAGGC	5	192	1
TGGCCTTGTTCTTGAAGGCTATTTAGAATCTCTT	5	207	1
AAAAAAAGCAAGTGAAGAGATTCTAAATAGCCTT	5	221	0
          ** ** * * ****
MAP Score: 10.5145

Motif 3
CATTTCAGAATATTTGCCAGAACCGTTATG	1	50	0
CTCTACTGGCTATGTGCCGGGTAGCATGAA	2	44	0
         TGATTTCTCGCGCGGGCAATC	4	1	1
GCGCGGGCAAGATTGCCCGCGCGAGAAATC	4	11	0
CCGCGCTTCTGCTCTCCCGGCGTAACCCGG	4	35	1
GCGTAACCCGGATTTGCCGCTTATACTTGT	4	54	1
TGAACGTGTCCATTTGCCACAAGTATAAGC	4	72	0
          GATTGGCCTGCGTTCAAAAA	5	0	1
GGCATATCCCGCTATGCCATTTTATTTTTG	5	24	0
GGCATAGCGGGATATGCCGCGAGCGGGCGA	5	36	1
AATCACCTAAAATCGCCCGCTCGCGGCATA	5	48	0
          **********
MAP Score: 8.60169

Motif 4
AAAAAAAAGCCCGCTCATTAGGCGGGCTGGGTATCTGAT	0	41	0
AAAAAACATTATCCAGAACGGGAGTGCGCC         	1	1	0
ATTTGCCAGAACCGTTATGATGTCGGCGCAAAAAACATT	1	30	0
  TGTTAACTCCTGCTAAATTGTTGGCGCTAATTATTTC	2	8	1
  GGCGGCTCCGGTACAAAAGAACCGCGCTATT      	3	4	0
AGCAGAAGCGCGGGCAAGATTGCCCGCGCGAGAAATCA 	4	9	0
GCGGCAAATCCGGGTTACGCCGGGAGAGCAGAAGCGCGG	4	35	0
AATGGCATAGCGGGATATGCCGCGAGCGGGCGATTTTAG	5	33	1
ATTTTGATCACGGAATAAAAAGTGATCGTCAGGTTACAT	5	136	1
          ***   *    * * ****
MAP Score: 5.30253

Motif 5
GGCTGGGTATCTGATTGCTTTACGCATGGTGAATAC	0	20	0
AATGAGCGGGCTTTTTTTTGAACAAAATTAGAGAAT	0	61	1
AGTTCGATGATTAATTGTCAACAGCTCATTTCAGAA	1	70	0
ATTGTTGGCGCTAATTATTTCATGCTACCCGGCACA	2	26	1
GCTATGCCATTTTATTTTTGAACGCAGGCCAATC  	5	8	0
CTGACGATCACTTTTTATTCCGTGATCAAAATCACC	5	132	0
AAGGGATGGCCTTGTTCTTGAAGGCTATTTAGAATC	5	201	1
ATCTCTTCACTTGCTTTTTTTCTGCTCTGTTTGTTA	5	234	1
TTTTTCTGCTCTGTTTGTTAAGGAAATCTC      	5	250	1
          **  ** **  * ***
MAP Score: 1.7568