AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID038_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391345
 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	ugpA	97	sn-glycerol 3-phosphate transport system, integral membrane protein
#5	ugpB	300	sn-glycerol 3-phosphate transport system; periplasmic binding protein

Motif 1
TAATTCGCTAACTCATCCTGGCATGTTGCTGT	0	19	1
ACGCGCCGCCGCTCATCGTCTAAGGAGTACTT	1	31	1
TAAATCTCAGGCGTATAATGGATGGCAATTTT	2	31	1
AAAAAAAACGGCGCATAAGCGCCGCTCATGGT	3	18	0
CAGGGAAAAAGCGTATTTGTGAGCTGACGCAA	3	84	0
AAACCCTTGTGCTCAATTGACAGTTTATTTTC	3	142	1
GATAAGCGAAACGCATCCGACATTACACTGA 	4	9	0
GATGCGTTTCGCTTATCTGACCTGGCATCGCG	4	24	1
GATGCGCTTCGCTTATCCGGCCTACACGCGAT	4	50	0
GATAAGCGAAGCGCATCCGGCACAGTTCAGGA	4	65	1
GGCGTAAACGCCTTATCAGGCCTACAAGATCG	5	31	0
GGCGTTTACGCCGCATCCGGCATGAAACGATG	5	51	1
TCTACAGATTGCTCATCGTTTCATGCCGGATG	5	64	0
ATATTTTCCCGCTTATCCGTGCCCCATCTCCC	5	114	1
GCGTGAATTCGCGCATTCGGTACAACAAGAGA	5	270	1
          ******* * **
MAP Score: 22.9633

Motif 2
GCTTCGCTTATCCGGCCTACACGCGATGCCAGG	4	44	0
AAACGCCTTATCAGGCCTACAAGATCGTGCAAA	5	25	0
TTGTTAAATCTCAGGCGTATAATGGATGGCAAT	2	27	1
TTACGCCGCATCCGGCATGAAACGATGAGCAAT	5	56	1
TTCTATATTTTCCCGCTTATCCGTGCCCCATCT	5	110	1
GCGAAACGCATCCGACATTACACTGA       	4	3	0
ATTTCTGCGTTCAGGATTGTCCTGCTGAACTGT	0	113	0
CCGGCACAGTTCAGGAATTAACCGTA       	4	81	1
GTAGGCCTGATAAGGCGTTTACGCCGCATCCGG	5	38	1
AGAGTTTGATTCAGACCTTCTATATTTTCCCGC	5	93	1
ATGCGCGAATTCACGCGTTTTATGCTCGCGGGG	5	253	0
GTTTCGCTTATCTGACCTGGCATCGCGTGTAGG	4	29	1
AGGGTTTTAGTCACGCAGGAAATCATTTTTTAC	3	116	0
          ****** *  ***
MAP Score: 9.81602

Motif 3
ATGAGCGGCGGCGCGTTCGGACGCCGCCTGGATGTTA   	1	7	0
AAAAAAAACGGCGCATAAGCGCCGCTCATGGTGAATTCTT	3	10	0
TTTATTTTCTGCGGAGTAGTCTCTCGTTTC          	3	165	1
CAGTGTAATGTCGGATGCGTTTCGCTTATCTGACCTGGCA	4	11	1
CGGCCTACACGCGATGCCAGGTCAGATAAGCGAAACGCAT	4	25	0
GATGCGCTTCGCTTATCCGGCCTACACGCGATGCCAGGTC	4	42	0
GATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCG	4	65	1
GCCTGATAAGGCGTTTACGCCGCATCCGGCATGAAACGAT	5	42	1
ATATTTTCCCGCTTATCCGTGCCCCATCTCCCATTTTCCC	5	114	1
AGATGACAAGGCGGTGACGGCGTGGGTGAGGGAAAATGGG	5	143	0
TACCGAATGCGCGAATTCACGCGTTTTATGCTCGCGGGGT	5	252	0
          ***  * ***  *   *  *
MAP Score: 9.19464

Motif 4
CATCCAGGCGGCGTCCGAACGCGCCGCCGCTCATCGTCTA	1	13	1
  AAGAATTCACCATGAGCGGCGCTTATGCGCCGTTTTTT	3	8	1
CAGGGAAAAAGCGTATTTGTGAGCTGACGCAAATAATCTA	3	76	0
CGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCG	4	33	1
GTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAG	4	55	1
GATCTTGTAGGCCTGATAAGGCGTTTACGCCGCATCCGGC	5	32	1
ATATTTTCCCGCTTATCCGTGCCCCATCTCCCATTTTCCC	5	114	1
AGCATAAAACGCGTGAATTCGCGCATTCGGTACAACAAGA	5	260	1
          ** *      ****   ***
MAP Score: 7.75065

Motif 5
CTGCGTTCAGGATTGTCCTGCTGAACTGTTA	0	111	0
TGTTGTCCTCTTGATTTCTGCGTTCAGGATT	0	128	0
ATGCGCCGTTTTTTTTTCTGTCACACCTTAT	3	34	1
TGGTAAAAAATGATTTCCTGCGTGACTAAAA	3	114	1
AATTGACAGTTTATTTTCTGCGGAGTAGTCT	3	156	1
AGATTGCTCATCGTTTCATGCCGGATGCGGC	5	60	0
AGACCTTCTATATTTTCCCGCTTATCCGTGC	5	105	1
ACAAAAAAGTTATTTTTCTGTAATTCGAGCA	5	212	1
GCGAATTCACGCGTTTTATGCTCGCGGGGTA	5	251	0
          * *********
MAP Score: 6.88865

Motif 6
ATGAGCGGCGGCGCGTTCGGACGCCGCCTGGAT	1	14	0
ACCATGAGCGGCGCTTATGCGCCGTTTTTTTTT	3	18	1
ACCTGGCATCGCGTGTAGGCCGGATAAGCGAAG	4	43	1
GATAAGCGAAGCGCATCCGGCACAGTTCAGGAA	4	65	1
GCCTGATAAGGCGTTTACGCCGCATCCGGCATG	5	42	1
GCGTGAATTCGCGCATTCGGTACAACAAGAGAG	5	270	1
          **** *****  *
MAP Score: 5.30683

Motif 7
GGCGTCCGAACGCGCCGCCGCTCATCGTCT	1	22	1
AAATTGTTAAATCTCAGGCGTATAATGGAT	2	24	1
CCATGAGCGGCGCTTATGCGCCGTTTTTTT	3	19	1
GTAAAAAATGATTTCCTGCGTGACTAAAAC	3	116	1
TTGACAGTTTATTTTCTGCGGAGTAGTCTC	3	158	1
GGATGCGTTTCGCTTATCTGACCTGGCATC	4	23	1
GGATAAGCGAAGCGCATCCGGCACAGTTCA	4	64	1
TATATTTTCCCGCTTATCCGTGCCCCATCT	5	113	1
CGCGTGAATTCGCGCATTCGGTACAACAAG	5	269	1
          **********
MAP Score: 5.28879

Motif 8
TTAAATCTCAGGCGTATAATGGATGGCAAT	2	30	1
AAAAAAAAACGGCGCATAAGCGCCGCTCAT	3	21	0
TCGCTTATCCGGCCTACACGCGATGCCAGG	4	44	0
CGCCTTATCAGGCCTACAAGATCGTGCAAA	5	25	0
GGCCTGATAAGGCGTTTACGCCGCATCCGG	5	41	1
          **********
MAP Score: 3.80528

Motif 9
AACATCCAGGCGGCGTCCGAACGCGCCGCC	1	11	1
ACTCCTTAGACGATGAGCGGCGGCGCGTTC	1	29	0
 AAGAATTCACCATGAGCGGCGCTTATGCG	3	9	1
CATGAGCGGCGCTTATGCGCCGTTTTTTTT	3	20	1
ATGCCAGGTCAGATAAGCGAAACGCATCCG	4	22	0
CGTGTAGGCCGGATAAGCGAAGCGCATCCG	4	54	1
CTGAACTGTGCCGGATGCGCTTCGCTTATC	4	65	0
GCCGGATGCGGCGTAAACGCCTTATCAGGC	5	42	0
GATGGGGCACGGATAAGCGGGAAAATATAG	5	112	0
AGGGAAAATGGGAGATGGGGCACGGATAAG	5	125	0
GTGACGGCGTGGGTGAGGGAAAATGGGAGA	5	140	0
GATGACAAGGCGGTGACGGCGTGGGTGAGG	5	152	0
TCTTGTTGTACCGAATGCGCGAATTCACGC	5	270	0
          **********
MAP Score: 1.43147

Motif 10
TGAGCGGCGGCGCGTTCGGACGCCGCCTGGAT	1	14	0
TTAAATCTCAGGCGTATAATGGATGGCAATTT	2	30	1
CACCATGAGCGGCGCTTATGCGCCGTTTTTTT	3	17	1
GACCTGGCATCGCGTGTAGGCCGGATAAGCGA	4	42	1
GGCCTGATAAGGCGTTTACGCCGCATCCGGCA	5	41	1
TCTATATTTTCCCGCTTATCCGTGCCCCATCT	5	111	1
GAGCATAAAACGCGTGAATTCGCGCATTCGGT	5	259	1
          ********  **
MAP Score: 1.39127