AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID056_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943391513
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	b0024	102	orf, hypothetical protein
#1	ileS	42	isoleucine tRNA synthetase
#2	pnp	177	polynucleotide phosphorylase; cytidylate kinase activity
#3	rpsO	148	30S ribosomal subunit protein S15
#4	rbfA	163	ribosome-binding factor A
#5	infB	24	protein chain initiation factor IF-2
#6	nusA	27	transcription pausing; L factor
#7	yhbC	300	orf, hypothetical protein

Motif 1
GTCAGCTTGAAAAAAGGGGCCACTCAGGCC	2	33	0
AATTAATTTTAAAAAGGGGCTAACAGCCCC	4	121	1
TCTCCTGACAAAAAAGGGGCTGTTAGCCCC	4	136	0
CCAAGACATAAAAAAAGGGCCTAAAGCCCA	7	278	0
GCGAGTTTCAGAAAAGGGGGCCTGAGTGGC	2	15	1
AAACCCCGATAAATCGGGGCTTTATATAAC	7	224	0
CCCCGCGCCTGAAACGTGGCAAATTCTACT	7	10	0
TGACTACAGAATAACTGGGCTTTAGGCCCT	7	263	1
CAAAAGAAGGCTAAAAGGGCATATTCCTCG	0	52	0
CAGTATATTTGAAAAAGGACTCTAAGGGAA	7	112	0
CCGTCTTGCGATAACAGGTCGCTACGAGTA	3	16	1
          **********
MAP Score: 19.4514

Motif 2
GTCAGCTTGAAAAAAGGGGCCACTCAGGCC	2	33	0
AATTAATTTTAAAAAGGGGCTAACAGCCCC	4	121	1
TCTCCTGACAAAAAAGGGGCTGTTAGCCCC	4	136	0
CAAGACATAAAAAAAGGGCCTAAAGCCCAG	7	277	0
GATTTGTGCAAATAAGCGCCGTTA      	0	88	1
GCGAGTTTCAGAAAAGGGGGCCTGAGTGGC	2	15	1
GTTCAGTTATATAAAGCCCCGATTTATCGG	7	219	1
TGGATGAGGTGAAAAGCCCGCG        	6	15	1
TTTACGCGACGTTAAGCGGCAGTATTCTAC	3	43	0
GTCAGATAACAAAAAACCCCGATAAATCGG	7	237	0
ACGTTGACCTGATAAGACGCGCCAGCGTCA	4	72	0
TTCCATGCGGGATAAGGCGTTTACGCTGCA	4	21	1
CTCTATGTGGGTAAAGCCTCTCATTAGCCG	2	128	0
TATATAGAATGAAAGGACGCCGATCTCTAA	3	113	0
          **********
MAP Score: 17.7862

Motif 3
GGCATGGATTGCCTGATGTGACGCTGGCGCGTCT	4	54	1
AGAAAAGGGGGCCTGAGTGGCCCCTTTTTTCAAG	2	24	1
TCCACCCCGCGCCTGAAACGTGGCAAATTCTACT	7	10	0
GTTCACGTTGACCTGATAAGACGCGCCAGCGTCA	4	72	0
AGGGTTCCATGCGGGATAAGGCGTTTACGCTGCA	4	17	1
GGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCATA	7	37	1
GGCAATCCATGCCGGATGCAGCGTAAACGCCTTA	4	33	0
AGGTTCGCGCGGCTAATGAGAGGCTTTACCCACA	2	119	1
GGTTGCGGGGGCCGGATTTGAACCGACGATCTTC	7	75	0
TAAAAAAAGGGCCTAAAGCCCAGTTATTCTGTAG	7	266	0
TTTAAAAAGGGGCTAACAGCCCCTTTTTTGTCAG	4	128	1
GAATACTGCCGCTTAACGTCGCGTAAATTGTTTA	3	46	1
GTCTGGATGAGGTGAAAAGCCCGCG         	6	12	1
TATCAGGTCAACGTGAACAGCCCTTCCACCTGAA	4	88	1
TAGCTCGTCGGGCTCATAACCCGAAGATCGTCGG	7	53	1
AGTGCTCCAGACCGCAGTTGCGGTTATAGGGTTC	7	189	1
GACAAAAGAAGGCTAAAAGGGCATATTCCTCGGC	0	50	0
          ******   * ***
MAP Score: 10.8371

Motif 4
CAAAGGCCGAGGAATATGCCCTTTTAGCCTTCTTT	0	45	1
AAAGGGGCCACTCAGGCCCCCTTTTCTGAAACTCG	2	16	0
AAAAGGGGGCCTGAGTGGCCCCTTTTTTCAAGCTG	2	26	1
TCAGGTCAACGTGAACAGCCCTTCCACCTGAAATT	4	90	1
AAAAAAGGGGCTGTTAGCCCCTTTTTAAAATTAAT	4	122	0
TTAAAAAGGGGCTAACAGCCCCTTTTTTGTCAGGA	4	129	1
AACCACTTTCCCTTAGAGTCCTTTTTCAAATATAC	7	105	1
GAATAACTGGGCTTTAGGCCCTTTTTTTATGTCTT	7	271	1
          *  *   ********
MAP Score: 8.86819

Motif 5
CTTGAAAAAAGGGGCCACTCAGGCCCCCTTTTCT	2	24	0
ATCTTCCGTTGCAGAGGTTCGCGCGGCTAATGAG	2	105	1
GAATACTGCCGCTTAACGTCGCGTAAATTGTTTA	3	46	1
 GGTTTTTAGGGTTCCATGCGGGATAAGGCGTTT	4	9	1
AGACGCGCCAGCGTCACATCAGGCAATCCATGCC	4	54	0
TGACGCTGGCGCGTCTTATCAGGTCAACGTGAAC	4	72	1
TTCAGGTGGAAGGGCTGTTCACGTTGACCTGATA	4	88	0
TGACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAA	4	127	0
GTCTGGATGAGGTGAAAAGCCCGCG         	6	12	1
AGTAGAATTTGCCACGTTTCAGGCGCGGGGTGGA	7	10	1
GAGCAGCCTGGTAGCTCGTCGGGCTCATAACCCG	7	42	1
GATTTGAACCGACGATCTTCGGGTTATGAGCCCG	7	61	0
GAAGATCGTCGGTTCAAATCCGGCCCCCGCAACC	7	75	1
          ** **   ******
MAP Score: 7.90677

Motif 6
TCCAACTCCCAAATGTGTTCTATATGGACAATTCAAAGGCCGA	0	12	1
GGACAATTCAAAGGCCGAGGAATATGCCCTTTTAGCCTTCTTT	0	37	1
GAGTTTCAGAAAAGGGGGCCTGAGTGGCCCCTTTTTTCAAGCT	2	17	1
TTCAGGTGGAAGGGCTGTTCACGTTGACCTGATAAGACGCGCC	4	79	0
AATTAATTTTAAAAAGGGGCTAACAGCCCCTTTTTTGTCAGGA	4	121	1
TCGTCGGTTCAAATCCGGCCCCCGCAACCACTTTCCCTTAGAG	7	80	1
GGGGCTTTATATAACTGAACCCTATAACCGCAACTGCGGTCTG	7	196	0
TGACTACAGAATAACTGGGCTTTAGGCCCTTTTTTTATGTCTT	7	263	1
          * * * *  *     * **  **
MAP Score: 5.36955

Motif 7
CAAAGGCCGAGGAATATGCCCTTTTAGCCTTCT	0	45	1
ATGGATTTGTGCAAATAAGCGCCGTTA      	0	85	1
GCGAGTTTCAGAAAAGGGGGCCTGAGTGGCCCC	2	15	1
CCGTCAGCTTGAAAAAAGGGGCCACTCAGGCCC	2	32	0
TTAGTTTCCAGTGAATTGCTGCCGTCAGCTTGA	2	53	0
ACCGTCTTGCGATAACAGGTCGCTACGAGTAGA	3	15	1
GCTACGAGTAGAATACTGCCGCTTAACGTCGCG	3	36	1
GGTTCCATGCGGGATAAGGCGTTTACGCTGCAT	4	19	1
TCAGGTCAACGTGAACAGCCCTTCCACCTGAAA	4	90	1
TTAAAAAGGGGCTAACAGCCCCTTTTTTGTCAG	4	129	1
TCTGGATGAGGTGAAAAGCCCGCG         	6	13	1
AGAATAACTGGGCTTTAGGCCCTTTTTTTATGT	7	270	1
          *  ** *******
MAP Score: 4.2737

Motif 8
TGACAAAAGAAGGCTAAAAGGGCATATTCCTCG	0	52	0
CAGAAAAGGGGGCCTGAGTGGCCCCTTTTTTCA	2	23	1
TATCAGGTCAACGTGAACAGCCCTTCCACCTGA	4	88	1
TTTTAAAAAGGGGCTAACAGCCCCTTTTTTGTC	4	127	1
AGTCTGGATGAGGTGAAAAGCCCGCG       	6	11	1
AGAATTTGCCACGTTTCAGGCGCGGGGTGGAGC	7	13	1
GGGGTGGAGCAGCCTGGTAGCTCGTCGGGCTCA	7	36	1
GACGATCTTCGGGTTATGAGCCCGACGAGCTAC	7	52	0
ACCGCAACTGCGGTCTGGAGCACTTTCCAGAAG	7	180	0
CAGAATAACTGGGCTTTAGGCCCTTTTTTTATG	7	269	1
          *****   *****
MAP Score: 3.59987

Motif 9
ATTGACAAAAGAAGGCTAAAAGGGCATATTCCTCG	0	52	0
CAATGGATTTGTGCAAATAAGCGCCGTTA      	0	83	1
TTGAAAAAAGGGGCCACTCAGGCCCCCTTTTCTGA	2	22	0
GTGGGTAAAGCCTCTCATTAGCCGCGCGAACCTCT	2	117	0
CTGGGTTAGGGTTGTCATTAGTCGCGAGG      	2	158	1
GTCGCTACGAGTAGAATACTGCCGCTTAACGTCGC	3	33	1
ATTTTAAAAAGGGGCTAACAGCCCCTTTTTTGTCA	4	126	1
TAGTCTGGATGAGGTGAAAAGCCCGCG        	6	10	1
GTAGAATTTGCCACGTTTCAGGCGCGGGGTGGAGC	7	11	1
CGACGATCTTCGGGTTATGAGCCCGACGAGCTACC	7	51	0
TACAGAATAACTGGGCTTTAGGCCCTTTTTTTATG	7	267	1
          * **   * ******
MAP Score: 3.43691

Motif 10
TTCAGAAAAGGGGGCCTGAGTGGCCCCTTTTTTC	2	21	1
TTCCGTTGCAGAGGTTCGCGCGGCTAATGAGAGG	2	108	1
TGCGGGATAAGGCGTTTACGCTGCATCCGGCATG	4	26	1
TGCCTGATGTGACGCTGGCGCGTCTTATCAGGTC	4	63	1
CTAAGGGAAAGTGGTTGCGGGGGCCGGATTTGAA	7	87	0
GACCGCAGTTGCGGTTATAGGGTTCAGTTATATA	7	198	1
          * ****   *****
MAP Score: 0.807734