AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons020_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242748
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ytgA	300	Solute Protein Binding Family
#1	CT406	300	hypothetical protein
#2	yebL	300	Solute-binding protein

Motif 1
AAAATTATTTAGAATTGTCTCTTCGAGATGAG	0	19	1
GCGATAAGCGAGGTTCTTTTTTTGGAGGGGGA	0	111	1
TCCTTACAGGAGGCTTGTATCCTTTAAAATAG	0	145	1
AAATATCGGTTGGTTTTTGTCCTTAGGGGATC	0	230	1
TCTTCTTAGAAAGGTTTTCTCTACGGGCGGTC	1	58	0
TTCTAAGAAGAGGTTCTTTTCAACACAAGACA	1	79	1
CACAAGACACAGGATTTTATCCATTAAAATAA	1	102	1
CAAGATACCACGGTTTTTATTTTAATGGATAA	1	118	0
TGATTTGTGGTGATTTTTTTTCAAAAGTCGCC	1	168	0
ATCACAATCAAGAATTGTGTTACTAGATCCCC	1	196	1
TTAGTTTTTTAAGATTTTATCTCCAGCTTTTT	2	71	1
TTTTGTTCAATGGCTTGTCTTCCAAACAATTT	2	231	0
          *** **** ***
MAP Score: 10.025

Motif 2
TTGTTAAAATTATTTAGAATTGTCTCTTCGAGATGAG	0	14	1
CGAGGTTCTTTTTTTGGAGGGGGAGCTCCTTACAGGA	0	119	1
AAAACTCTATTTTAAAGGATACAAGCCTCCTGTAAGG	0	146	0
GATCGTATACTTTTTCAAAGTATGTCCCCGTATCGAT	0	258	1
AAGAACCTCTTCTTAGAAAGGTTTTCTCTACGGGCGG	1	60	0
CTGTGTCTTGTGTTGAAAAGAACCTCTTCTTAGAAAG	1	77	0
CGGTTTTTATTTTAATGGATAAAATCCTGTGTCTTGT	1	103	0
AATATTTGAATTTTAGGAGGAATCTCCC         	1	282	1
TATTCTTAGTTTTTTAAGATTTTATCTCCAGCTTTTT	2	66	1
CCTCACCCCGTTTTCTAAAGCTTCTCTGCTCTGAACC	2	138	1
AGAATGAAATTGTTTGGAAGACAAGCCATTGAACAAA	2	225	1
          * **  ****    ***
MAP Score: 8.31441

Motif 3
CGAAGAGACAATTCTAAATAATTTTAACAACTAA    	0	6	0
AAATTCATTCTGTTAAAAGTATCTTTGCGATAAGCGAG	0	85	1
GCTTGTATCCTTTAAAATAGAGTTTTTCTTATGATCCC	0	157	1
ATCGTATACTTTTTCAAAGTATGTCCCCGTATCGATTA	0	259	1
TGTGTCTTGTGTTGAAAAGAACCTCTTCTTAGAAAGGT	1	75	0
ATTAGGCGACTTTTGAAAAAAAATCACCACAAATCACA	1	164	1
ATTCTTAGTTTTTTAAGATTTTATCTCCAGCTTTTTTC	2	67	1
TTGCTTTTTCTTTAAAAAACTGTTCCTCACCCCGTTTT	2	114	1
CTCACCCCGTTTTCTAAAGCTTCTCTGCTCTGAACCCC	2	139	1
GACAAGCCATTGAACAAAATTACTCAACAATAGAATAA	2	244	1
          ***  ***  *  **  *
MAP Score: 7.13659

Motif 4
TGAATTTATATCCTCAACCAAAAGGAAAATCT	0	60	0
CGCAAAGATACTTTTAACAGAATGAATTTATA	0	82	0
AAGGAGCTCCCCCTCCAAAAAAAGAACCTCGC	0	118	0
GAGGCTTGTATCCTTTAAAATAGAGTTTTTCT	0	154	1
GATCGTATACTTTTTCAAAGTATGTCCCCGTA	0	258	1
GTAGAGAAAACCTTTCTAAGAAGAGGTTCTTT	1	66	1
GAAGAGGTTCTTTTCAACACAAGACACAGGAT	1	85	1
AGGATTTTATCCATTAAAATAAAAACCGTGGT	1	112	1
TATTAGGCGACTTTTGAAAAAAAATCACCACA	1	163	1
 AAACTACTACTCTCCAAACAACTCGGCTATC	2	9	1
TTTTTGCTTTTTCTTTAAAAAACTGTTCCTCA	2	111	1
TTAACGCGATTTCCCTAAAGAATGAAATTGTT	2	207	1
CAATGGCTTGTCTTCCAAACAATTTCATTCTT	2	224	0
GGAAGACAAGCCATTGAACAAAATTACTCAAC	2	240	1
          ***** *** **
MAP Score: 6.96933

Motif 5
GGCTTGTATCCTTTAAAATAGAGTTTTTCT	0	156	1
CACATGGGATCATAAGAAAAACTCTATTTT	0	170	0
CGGGGACATACTTTGAAAAAGTATACGATC	0	258	0
GGATTTTATCCATTAAAATAAAAACCGTGG	1	113	1
TATTAGGCGACTTTTGAAAAAAAATCACCA	1	163	1
TTTGCTTTTTCTTTAAAAAACTGTTCCTCA	2	113	1
AGCAGAGAAGCTTTAGAAAACGGGGTGAGG	2	138	0
AATTACTCAACAATAGAATAATGGTTCGTT	2	261	1
          **********
MAP Score: 6.78276

Motif 6
CGCAAAGATACTTTTAACAGAATGAATTTATA	0	82	0
AGGAGCTCCCCCTCCAAAAAAAGAACCTCGCT	0	117	0
CCGAGACCGCCCGTAGAGAAAACCTTTCTAAG	1	54	1
CTGTGTCTTGTGTTGAAAAGAACCTCTTCTTA	1	82	0
GGATTTTATCCATTAAAATAAAAACCGTGGTA	1	113	1
TATTAGGCGACTTTTGAAAAAAAATCACCACA	1	163	1
GGCAAAAAGACAGTAGAAAGAATATTCTTAGT	2	44	1
AGGAACAGTTTTTTAAAGAAAAAGCAAAAATT	2	109	0
GAAGACAAGCCATTGAACAAAATTACTCAACA	2	241	1
          * ** *******
MAP Score: 1.95258