AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons015_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237907
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hisS	300	Histidyl tRNA Synthetase
#1	uhpC	243	Hexosphosphate Transport
#2	minD	32	chromosome partitioning ATPase
#3	thrS	199	Threonyl tRNA Synthetase
#4	alaS	232	Alanyl tRNA Synthetase
#5	CPn0925	159	CT779 hypothetical protein
#6	lysS	300	Lysyl tRNA Synthetase

Motif 1
GTATTTCTTATTTAATTAAAAATAACCAAGAAAA	1	84	1
ATAAAAGTTTTTTTATAAAAAAAAGCTTCTTGCT	3	110	1
AGCTTCTTGCTTTGATCAAAAAAAACACTAAAAT	3	133	1
GCGAAATGCCCTTCATTAAAAAGAGGGTAGATTC	0	184	1
TACCTTGTAATTCTTTCAAAAACAAATGAATTTT	4	83	1
CGCATTTCATCTCAGTGAAAAAGATTTTACACAT	1	207	1
ATCCCTAATTTTTAGTTAAAAAACTTTCCTGTTT	4	135	0
     GTCACTATCCTTAAAAAAACGTGTCGAAT	5	5	1
AATAGCCAATGTTTCTAAAAAAGAGAGGTACGTT	5	134	0
TGTAAACATGCTTCTTAATAAAGAATTTTAAGAA	0	30	1
CTTTGGAACTTGTATTAAAAAATAAAAGTTTTTT	3	89	1
TTCTCCAATACTTAGTTACAAAAACCATAAGCTA	0	93	1
TCTTGATGCGTATCCTCAAAAATCCTTAGCAA  	2	8	0
TCGATCAAATCTCAATAATAAACAGGAAAGTTTT	4	116	1
  GTGATGTCTTCGCTCAAAATGATTACTTTTTT	0	278	0
CCTGGAGACCTTCTATGTAAAAGCAGCAACTATA	4	18	1
CCAGATATTCCATTATCTAAAAAAGTAATCATTT	0	260	1
          ***  * ***** *
MAP Score: 16.5824

Motif 2
AATGTTTCTAAAAAAGAGAGGTACGTTTTG	5	131	0
GCCCTTCATTAAAAAGAGGGTAGATTCGAG	0	191	1
TTTACAGACGAAAACAAAAGATAATT    	0	6	0
TTATAGAAGTAAAACAAGAGCTGTACTACC	6	38	1
ATCCCCAAGCAAAAAGCAAGGAACTCTTAC	4	56	1
CTAAAGTTGTAAAAAGCAGGCCGATCCCAC	6	216	0
TTCCCCGAGCAAAACCAAGGCCTATATTCT	6	72	0
ATCAAGGATGAAAAAACAAGGAGGGAATCG	1	156	0
TGGTACCCATAAAAGGAGAGCTCTCTGTGG	5	103	0
TAAAATGCTAACAACGAAAGTCCCCCTAAC	3	161	1
AATTCTTTCAAAAACAAATGAATTTTCGAT	4	91	1
CTTTAGATTCATAAAGAAAGATATCATGGA	6	104	0
CTTGTATTAAAAAATAAAAGTTTTTTTATA	3	97	1
AGTTTTTTTATAAAAAAAAGCTTCTTGCTT	3	115	1
ACTATCCTTAAAAAAACGTGTCGAATAAGT	5	13	1
TTTTTTTTGATCAAAGCAAGAAGCTTTTTT	3	128	0
          **********
MAP Score: 11.5473

Motif 3
GCTTCTTAATAAAGAATTTTAAGAATAGTT	0	39	1
ATAACCAAGAAAAACACTCTACTAATGCAT	1	105	1
TTTTTTTATAAAAAAACTTTTATTTTTTAA	3	103	0
TGATCAAAGCAAGAAGCTTTTTTTTATAAA	3	121	0
CTTTGATCAAAAAAAACACTAAAATGCTAA	3	142	1
AGCAAAAAGCAAGGAACTCTTACCTTGTAA	4	63	1
ATTTTTAGTTAAAAAACTTTCCTGTTTATT	4	132	0
AGACGAAAATAAAGAACTCTCCTATAATGG	4	171	1
       GAAAAAGAACTCTCAACGGCAGC	4	219	0
TCTTATCCACAGAGAGCTCTCCTTTTATGG	5	97	1
          **********
MAP Score: 9.91589

Motif 4
TGTTTTAGTATTTCTTATTTAATTAAAAATAACCAAG	1	77	1
TAAAAAAACTTTTATTTTTTAATACAAGTTCCAAAGC	3	88	0
AAAATAAAAGTTTTTTTATAAAAAAAAGCTTCTTGCT	3	107	1
TTTTAGTGTTTTTTTTGATCAAAGCAAGAAGCTTTTT	3	129	0
CTTGTAATTCTTTCAAAAACAAATGAATTTTCGATCA	4	86	1
ACAGGAAAGTTTTTTAACTAAAAATTAGGGATAGAGA	4	137	1
TCTATTCTTATTTTATCCTAAATCAGATAATAGTGTC	5	57	0
CCATGATATCTTTCTTTATGAATCTAAAGTTTTCCTA	6	105	1
          *** **  * ***   *
MAP Score: 1.04184