AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons019_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242709
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
TTGTTAAAACAGCCCTTTTCCACAAAATAC	0	83	1
ACTAGGGATGAGTCCTTTCCCAAAGGCCTT	0	139	1
CCTTTCCCAAAGGCCTTCTTAAGACCTTCC	0	152	1
GGCCTTCTTAAGACCTTCCTTGACTTCGGT	0	163	1
AGGAGTTGGTACAGCTTCTTGTTTTGCTGA	0	212	1
ATAACATGGAAGCGCTTCTTATAGAGTAGC	2	70	1
          **********
MAP Score: 3.94061

Motif 2
AAAAAGAATACTAGAAGTTTTTGATTTGGAGAGCC	0	14	0
GGGAAACGTGCATAGTATATATACTAAAAAGAATA	0	39	0
ATTTTGTGGAAAAGGGCTGTTTTAACAACTGGTGA	0	76	0
TCCAGCTAAACTAGGGATGAGTCCTTTCCCAAAGG	0	130	1
TAAGACCTTCCTTGACTTCGGTTCATCCGTAATAA	0	171	1
TAATAAGTTTCAAGGAGTTGGTACAGCTTCTTGTT	0	200	1
AACCCTAGCAGTTGAAGTGTTTTCATTATTTTCAG	0	238	0
ACTTCAACTGCTAGGGTTATCTTATATAG      	0	255	1
TAATCTAAGGCATAGAGTATATGCATTCTCGAAAA	1	45	0
GTTTCGATAACATGGAAGCGCTTCTTATAGAGTAG	2	64	1
CTTCCAATAACTAGAGATAGCTACTCTATAAGAAG	2	84	0
ACTCCTAAGCATTGACCTTGCTTCTTCCAATAACT	2	107	0
          *****  * * * **
MAP Score: 3.67918

Motif 3
ATATATACTAAAAAGAATACTAGAAGTTTTTGATTTGGAGAGCCAA	0	12	0
CTAGTTTAGCTGGAAGACAGTTAATGGCAAAGTATTTTGTGGAAAA	0	98	0
AATAAGTTTCAAGGAGTTGGTACAGCTTCTTGTTTTGCTGAAAATA	0	201	1
GCTGAAAATAATGAAAACACTTCAACTGCTAGGGTTATCTTATATA	0	237	1
          ACGTATGTAATATATATTTTCGGGTTCGAAGAAAAT	1	0	1
ATTTTCGAGAATGCATATACTCTATGCCTTAGATTAAGGAGAGTGT	1	44	1
ACTTTTTGAAAAAAAGTTACTGAAAAATAATCAGTTTCGATAACAT	2	31	1
CAATAACTAGAGATAGCTACTCTATAAGAAGCGCTTCCATGTTATC	2	69	0
AGTTATTGGAAGAAGCAAGGTCAATGCTTAGGAGTTTTTA      	2	107	1
          * * *   ***  *       *  **
MAP Score: 2.72011