AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons019_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242717
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ybbP	274	hypothetical protein
#1	ung	80	Uracil DNA Glycosylase
#2	ctc	300	General Stress Protein
#3	rs6	137	S6 Ribosomal Protein

Motif 1
GTTGTTAAAACAGCCCTTTTCCACAAAATA	0	82	1
AACTAGGGATGAGTCCTTTCCCAAAGGCCT	0	138	1
TCCTTTCCCAAAGGCCTTCTTAAGACCTTC	0	151	1
AGGCCTTCTTAAGACCTTCCTTGACTTCGG	0	162	1
   GAGGTTCGAATCCTTCCACCCCAGAGT	2	7	1
ATTTTCGATTGGGGCCATCTAAGGGAACAG	2	94	1
TGATTATTATCAAGCCTTCTGTTCCCTTAG	2	112	0
GTGCCATTTTAAGGCCGTCTGGTATAGCGC	2	193	1
TATAGCGCGTAGGACCGTTCATCCGGTTGA	2	215	1
GAATGGCCTTAAGGGCTTCTTTTCCCTCAA	2	241	0
AGAAGCCCTTAAGGCCATTCAAAGGCCTTT	2	251	1
AGGCCATTCAAAGGCCTTTTAGCTCAAGGT	2	262	1
ACTCTATAAGAAGCGCTTCCATGTTATCGA	3	67	0
          **********
MAP Score: 16.1557

Motif 2
CCCTGTCACCAGTTGTTAAAACAGCCCTTTTCC	0	71	1
ATGGCAAAGTATTTTGTGGAAAAGGGCTGTTTT	0	88	0
GCTGGAAGACAGTTAATGGCAAAGTATTTTGTG	0	103	0
TGTTTTCATTATTTTCAGCAAAACAAGAAGCTG	0	223	0
TATATTTTCGGGTTCGAAGAAAATTTTCGAGAA	1	22	1
CCGTTCATCCGGTTGAGGGAAAAGAAGCCCTTA	2	229	1
TTTACTGTTCACTTTTTGAAAAAAAGTTACTGA	3	21	1
TTTGAAAAAAAGTTACTGAAAAATAATCAGTTT	3	35	1
AAAAATAATCAGTTTCGATAACATGGAAGCGCT	3	53	1
AGCTATCTCTAGTTATTGGAAGAAGCAAGGTCA	3	97	1
          ****  ** ****
MAP Score: 5.94462

Motif 3
ATACTAGAAGTTTTTGATTTGGAGAGCCAAAT  	0	8	0
TAATATATATTTTCGGGTTCGAAGAAAATTTTCG	1	17	1
TGTGAATCTCTTATTGAATAGGAGAGATTTTCGA	2	68	1
TGGGGCCATCTAAGGGAACAGAAGGCTTGATAAT	2	103	1
TTCATCCGGTTGAGGGAAAAGAAGCCCTTAAGGC	2	232	1
GCCTTTTAGCTCAAGGTAATGGAGAATAGCATTT	2	275	1
TACTGTTCACTTTTTGAAAAAAAGTTACTGAAAA	3	23	1
AGAAGCAAGGTCAATGCTTAGGAGTTTTTA    	3	117	1
          * * ** * *****
MAP Score: 4.97484

Motif 4
TTAGCTGGAAGACAGTTAATGGCAAAGTATTTTGTGG	0	102	0
AAGGTCTTAAGAAGGCCTTTGGGAAAGGACTCATCCC	0	143	0
GTAATAAGTTTCAAGGAGTTGGTACAGCTTCTTGTTT	0	199	1
TTCGATTGGGGCCATCTAAGGGAACAGAAGGCTTGAT	2	97	1
ATACCAGACGGCCTTAAAATGGCACATACGAAGAAAT	2	181	0
TTTAAGGCCGTCTGGTATAGCGCGTAGGACCGTTCAT	2	200	1
GGACCGTTCATCCGGTTGAGGGAAAAGAAGCCCTTAA	2	226	1
GCCTTTTAGCTCAAGGTAATGGAGAATAGCATTTT  	2	275	1
ATAATCAGTTTCGATAACATGGAAGCGCTTCTTATAG	3	57	1
AGTAGCTATCTCTAGTTATTGGAAGAAGCAAGGTCAA	3	94	1
          **  *   **** * **
MAP Score: 4.60412

Motif 5
TCTTCGTATGTGCCATTTTAAGGCCGTCTGGTATA	2	184	1
AAGCCCTTAAGGCCATTCAAAGGCCTTTTAGCTCA	2	253	1
CTTTCCCAAAGGCCTTCTTAAGACCTTCCTTGACT	0	153	1
AAGCCTTCTGTTCCCTTAGATGGCCCCAATCGAAA	2	96	0
CAAAATACTTTGCCATTAACTGTCTTCCAGCTAAA	0	105	1
TTGTCTTTTATTCCCCCTTAGGTCTGGTTTAATGT	2	36	1
AGGGCTTCTTTTCCCTCAACCGGATGAACGGTCCT	2	225	0
          **** **  * * **
MAP Score: 4.03948

Motif 6
GATGAGTCCTTTCCCAAAGGCCTTCTTAAGACCTTCCTTG	0	145	1
CTTCCTTGACTTCGGTTCATCCGTAATAAGTTTCAAGGAG	0	177	1
CATTAAACCAGACCTAAGGGGGAATAAAAGACAACTCTGG	2	30	0
AGGAGAGATTTTCGATTGGGGCCATCTAAGGGAACAGAAG	2	87	1
AGAGGATTTCTTCGTATGTGCCATTTTAAGGCCGTCTGGT	2	176	1
GGACCGTTCATCCGGTTGAGGGAAAAGAAGCCCTTAAGGC	2	226	1
GGGAAAAGAAGCCCTTAAGGCCATTCAAAGGCCTTTTAGC	2	245	1
          * **    ****     ***
MAP Score: 2.88844

Motif 7
CTGTCTTCCAGCTAAACTAGGGATGAGTCCTTT	0	124	1
TTTCCCAAAGGCCTTCTTAAGACCTTCCTTGAC	0	154	1
TGTCTTTTATTCCCCCTTAGGTCTGGTTTAATG	2	37	1
TTCGATTGGGGCCATCTAAGGGAACAGAAGGCT	2	97	1
CTTCGTATGTGCCATTTTAAGGCCGTCTGGTAT	2	185	1
GGACCGTTCATCCGGTTGAGGGAAAAGAAGCCC	2	226	1
AGCCCTTAAGGCCATTCAAAGGCCTTTTAGCTC	2	254	1
          ***  ** *****
MAP Score: 1.22111