AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons013_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242395
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	glgX	117	Glycogen Hydrolase (debranching)
#1	sycE	37	Secretion Chaperone
#2	yscU	256	YopS Translocation Protein U
#3	glgP	155	Glycogen Phosphorylase
#4	glgC	192	Glucose-1-P Adenyltransferase
#5	glgA	300	Glycogen Synthase
#6	mrsA	245	Phosphoglucomutase
#7	CT865	248	hypothetical protein

Motif 1
TTCGGTTAGATTTTTATTAAACTTACTTGTT	0	87	1
AAGTGCGCTCTTTTTATTACAGTTTTTACAA	1	11	0
GTTGTACAGCTTTTTCTTAAGGCTAACACAG	2	20	1
TAACACAGCCTTTTTATTATTAAGGAAAAAG	2	43	1
CTAATCTTGCTTTTTCTTTAGAATTTCTTTT	2	69	0
GAACGGAATATTTTTTTTAAAGAGCGTTTTT	2	109	0
TATATAAATGTTTTTCTCAAGAAAGAAGGTG	2	187	0
TGTTCGCCTTTTTTAGTTAAGGAGGCTTT  	3	8	0
AATAGAAATCTTTCTTTTAATATTAATATTT	3	93	1
TTAATATTAATATTTCTTATTCACAAGCAAA	3	109	1
ATGGGTCCGTTTTTTGTCAAAATTAGATAAT	4	48	1
AATTAGATAATTTTTATTTTTCAAACATCTA	4	68	1
AATAAATCGATTTTATTTTTAGATGTTTGAA	4	87	0
TTGTCTGGCTTTTTTAATAATTTATTTTTTA	4	143	1
TTTAATAATTTATTTTTTAAAATTATTTTTT	4	155	1
TTTTTAAAATTATTTTTTATGGTGGCGGGGA	4	168	1
AAAATCAAAGTTTTTTACATTTAAGGGGCAT	5	138	1
ATTTAATTACTTTTATTTAATGGATAGTTTC	5	198	0
AATCAAGATGTTTTTGTTATATTTAATTACT	5	218	0
ATCTTGATTATTTTTGTTAAAAGAAATAATT	5	240	1
AATTAATGAGTTTTATTTAATTAACGAAACG	5	267	1
TGATTTATTTTTTTTGTTTTT          	6	0	0
GCCATTCACTTTTTAAATAAGAAGTAAGAAA	6	50	0
ATATTCCCTATTTTTATCAAAATCTTTGCAA	6	162	0
GCACGAGCAATTTTTTATAAGGATAAACATT	7	41	1
CAAAATAAGATTTCTTTTAATTACGAGTGTA	7	104	1
          ***** *****
MAP Score: 30.5113

Motif 2
CTTCTTATTTAAAAAGTGAATGGCCGTTTGAATTTTTGTTTGG	6	57	1
TTTCCTCCTGACAAAATAAGATTTCTTTTAATTACGAGTGTAG	7	93	1
TGCATGAATAATAAATCGATTTTATTTTTAGATGTTTGAAAAA	4	84	0
AAAGATTTTGATAAAAATAGGGAATATTTATCTCTGAAAATCA	6	166	1
TATCCTTATAAAAAATTGCTCGTGCTTTTATCTTGCAAATATT	7	23	0
GTTAATTAAATAAAACTCATTAATTATTTCTTTTAACAAAAAT	5	249	0
CCGTTTTTTGTCAAAATTAGATAATTTTTATTTTTCAAACATC	4	54	1
TAAATATAACAAAAACATCTTGATTATTTTTGTTAAAAGAAAT	5	224	1
GAGAAATTTCTCAAAAATCAAAGTTTTTTACATTTAAGGGGCA	5	125	1
TTTCTTATTCACAAGCAAACAAACTCTTTACATGAGAAGCCTC	3	121	1
AAAACGCTCTTTAAAAAAAATATTCCGTTCTCTAAAGAACCCC	2	110	1
TATTTATCTCTGAAAATCAAGGATCAGTTAGTTTTGAGCCAAA	6	190	1
CACAAAAGGAAGAGAGACCCTCTTCCTTTTGTTGTATGATAGC	0	17	0
TCCGTTCTCTAAAGAACCCCTTACTCTTTGTTTATAAATGGGA	2	133	1
CTTATCTCTATAAAGGGCATGGGTCCGTTTTTTGTCAAAATTA	4	30	1
AGCTTTTTCTTAAGGCTAACACAGCCTTTTTATTATTAAGGAA	2	27	1
TCGTCTGTTGAGAATAGAAATCTTTCTTTTAATATTAATATTT	3	81	1
      AAAAACAAAAAAAATAAATCATTTAGTTTTCGATAAT	6	4	1
AAAAATCAAGTAAAATGTTCGCCTTTTTTAGTTAAGGAGGCTT	3	11	0
          AAAGGAAGTGCGCTCTTTTTATTACAGTTTTTA	1	14	0
          * ***   *     * ***   *
MAP Score: 17.4773

Motif 3
TTCTTGAGAAAAACATTTATATACGGTAACTTG	2	195	1
ATATTAAAAGAAAGATTTCTATTCTCAACAGAC	3	83	0
TTTATTTTTCAAACATCTAAAAATAAAATCGAT	4	80	1
CTACCGATAAAAAGGTTTTGTGAGGTACACTCG	5	93	0
CTCAAAAATCAAAGTTTTTTACATTTAAGGGGC	5	134	1
AATATAACAAAAACATCTTGATTATTTTTGTTA	5	226	1
ATGTTTGAGGAAAGGTCTTAAGAAGGCGAATTG	6	132	1
GGCGAATTGCAAAGATTTTGATAAAAATAGGGA	6	156	1
TTATAAGGATAAACATTTTTAGAATAGAAGAAA	7	55	1
ATGTTGATAATAACGTTTCTAAAAGGTACCATG	7	145	1
TGATTAAATATAAGGTCTGGAGAGGATAGTACA	7	208	1
          ********  * *
MAP Score: 6.65179

Motif 4
AAAAGGAAGAGAGACCCTCTTCCTTTTGTTG	0	26	0
ATTTTTTTTAAAGAGCGTTTTTCATGAAGCA	2	100	0
CCGTTCTCTAAAGAACCCCTTACTCTTTGTT	2	134	1
ATGAGCATCTGCCACCTTCTTTCTTGAGAAA	2	175	1
CTTTCTTGAGAAAAACATTTATATACGGTAA	2	193	1
ACTAAAAAAGGCGAACATTTTACTTGATTTT	3	22	1
ACCGAATATCAAGACCCTCTGCAGTATCGTC	3	55	1
TCACAAGCAAACAAACTCTTTACATGAGAAG	3	129	1
TTATAGAGATAAGAACTCTTTTCTGACTCGC	4	12	0
GCGCGGTACCAAAAACCGCTGCCTTACCGCT	5	38	1
TGTACCTCACAAAACCTTTTTATCGGTAGAG	5	97	1
TACCACCACAACGACCTTCTATGAGCAGAAA	5	171	1
TAAATATAACAAAAACATCTTGATTATTTTT	5	224	1
TATCAACATAGCGACCTCCTACACTCGTAAT	7	123	0
          ****** ****
MAP Score: 2.03596