AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID023_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391137
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	pspA	151	phage shock protein, inner membrane protein
#1	pspB	53	phage shock protein
#2	pspE	74	phage shock protein
#3	ycjM	185	putative polysaccharide hydrolase
#4	ycjQ	30	putative oxidoreductase
#5	ugpA	97	sn-glycerol 3-phosphate transport system, integral membrane protein
#6	ugpB	300	sn-glycerol 3-phosphate transport system; periplasmic binding protein

Motif 1
GATAAGCGAAGCGCATCCGGCACAGTTCAGG	5	65	1
GGCGTTTACGCCGCATCCGGCATGAAACGAT	6	51	1
GATGCGCTTCGCTTATCCGGCCTACACGCGA	5	51	0
CTCACCCACGCCGTCACCGCCTTGTCATCTT	6	153	1
GCGTCCGAACGCGCCGCCGCTCATCGTCTAA	1	23	1
GCGTGAATTCGCGCATTCGGTACAACAAGAG	6	270	1
CATGAGCGGCGCTTATGCGCCGTTTTTTTTT	3	20	1
GGCGTAAACGCCTTATCAGGCCTACAAGATC	6	32	0
GATAAGCGAAACGCATCCGACATTACACTGA	5	10	0
          ***** *****
MAP Score: 11.8954

Motif 2
AACAGTTCAGCAGGACAATCCTGAACGCAGAAATCAA	0	112	1
GCGGCGCGTTCGGACGCCGCCTGGATGTTA       	1	3	0
AATTGCCATCCATTATACGCCTGAGATTTAACAATTT	2	24	0
AAGAATTCACCATGAGCGGCGCTTATGCGCCGTTTTT	3	10	1
ATGCGCTTCGCTTATCCGGCCTACACGCGATGCCAGG	5	44	0
        TACGGTTAATTCCTGAACTGTGCCGGATG	5	78	0
GCGTAAACGCCTTATCAGGCCTACAAGATCGTGCAAA	6	25	0
CGTTTCATGCCGGATGCGGCGTAAACGCCTTATCAGG	6	43	0
GATGACAAGGCGGTGACGGCGTGGGTGAGGGAAAATG	6	145	0
CGCGGGGTAACATGACATGCTCGAATTACAGAAAAAT	6	223	0
ACCCCGCGAGCATAAAACGCGTGAATTCGCGCATTCG	6	252	1
          * *   * ***** * *
MAP Score: 9.54628

Motif 3
AACAGTTCAGCAGGACAATCCTGAACGCAGAAATCAAGA	0	112	1
   TAACATCCAGGCGGCGTCCGAACGCGCCGCCGCTCA	1	7	1
TGTTAAATCTCAGGCGTATAATGGATGGCAATTTTCATC	2	28	1
AAGAATTCACCATGAGCGGCGCTTATGCGCCGTTTTTTT	3	10	1
         TCAGTGTAATGTCGGATGCGTTTCGCTTAT	5	1	1
CTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGA	5	35	1
CGGTTAATTCCTGAACTGTGCCGGATGCGCTTCGCTTAT	5	66	0
TATGTTGAATTTGCACGATCTTGTAGGCCTGATAAGGCG	6	16	1
AGATTGCTCATCGTTTCATGCCGGATGCGGCGTAAACGC	6	52	0
ACCCCGCGAGCATAAAACGCGTGAATTCGCGCATTCGGT	6	252	1
CGTTTATCTCTCTTGTTGTACCGAATGCGCGAATTCACG	6	271	0
          * *     *  ** *****
MAP Score: 9.29837

Motif 4
ATCCTGAACGCAGAAATCAAGAGGACAACA	0	129	1
TAAGGTGTGACAGAAAAAAAAACGGCGCAT	3	34	0
CATTTTTTACCAGGGAAAAAGCGTATTTGT	3	96	0
TTTAGTCACGCAGGAAATCATTTTTTACCA	3	114	0
GACTACTCCGCAGAAAATAAACTGTCAATT	3	156	0
CGGCACAGTTCAGGAATTAACCGTA     	5	82	1
CACGGATAAGCGGGAAAATATAGAAGGTCT	6	105	0
GCTCGAATTACAGAAAAATAACTTTTTTGT	6	212	0
          **********
MAP Score: 7.1747

Motif 5
ATGAGCGGCGGCGCGTTCGGACGCCGCCTGGATGTTA 	1	9	0
GCGCTTATGCGCCGTTTTTTTTTCTGTCACACCTTATT	3	28	1
CAGGGAAAAAGCGTATTTGTGAGCTGACGCAAATAATC	3	78	0
  TTAAAACTCCTTGTAAAGAAACTGGCCGCT      	4	4	0
AATGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGC	5	17	1
TGTGCCGGATGCGCTTCGCTTATCCGGCCTACACGCGA	5	51	0
TTGATTCAGACCTTCTATATTTTCCCGCTTATCCGTGC	6	98	1
GCCCCATCTCCCATTTTCCCTCACCCACGCCGTCACCG	6	134	1
GCCGTCACCGCCTTGTCATCTTTCTGACACCTTACTAT	6	162	1
TGTAATTCGAGCATGTCATGTTACCCCGCGAGCATAAA	6	230	1
          ** * *   **  *** *
MAP Score: 6.98894

Motif 6
CATCCAGGCGGCGTCCGAACGCGCCGCCGCTCATCGTCTA	1	13	1
GATCTTGTAGGCCTGATAAGGCGTTTACGCCGCATCCGGC	6	32	1
CAGGGAAAAAGCGTATTTGTGAGCTGACGCAAATAATCTA	3	76	0
CGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCG	5	33	1
AGCATAAAACGCGTGAATTCGCGCATTCGGTACAACAAGA	6	260	1
  AAGAATTCACCATGAGCGGCGCTTATGCGCCGTTTTTT	3	8	1
GCGTGGGTGAGGGAAAATGGGAGATGGGGCACGGATAAGC	6	124	0
GGTGTCAGAAAGATGACAAGGCGGTGACGGCGTGGGTGAG	6	153	0
          ****      ***  *  **
MAP Score: 5.7626

Motif 7
GCTAACTCATCCTGGCATGTTGCTGTTGATT	0	25	1
GAACGCGCCGCCGCTCATCGTCTAAGGAGTA	1	29	1
CGCATAAGCGCCGCTCATGGTGAATTCTT  	3	8	0
GCTTATCTGACCTGGCATCGCGTGTAGGCCG	5	34	1
ACTCTACAGATTGCTCATCGTTTCATGCCGG	6	67	0
CCGTCACCGCCTTGTCATCTTTCTGACACCT	6	163	1
GTAATTCGAGCATGTCATGTTACCCCGCGAG	6	231	1
          * *********
MAP Score: 4.7907

Motif 8
TAACTCATCCTGGCATGTTGCTGTTGATTCTTCAATCAGATCTT	0	27	1
GTATAATGGATGGCAATTTTCATCCATAGAAGGACGCTTAC   	2	43	1
TGTGCTCAATTGACAGTTTATTTTCTGCGGAGTAGTCTCTCGTT	3	149	1
TTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCA	5	36	1
          TGGCAATATGTTGAATTTGCACGATCTTGTAGGC	6	0	1
GTCACCGCCTTGTCATCTTTCTGACACCTTACTATCTTACAAAT	6	165	1
AATTCGAGCATGTCATGTTACCCCGCGAGCATAAAACGCGTGAA	6	233	1
          *****   * *       * *  *
MAP Score: 1.25934