AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons007_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237507
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rs21	178	S21 Ribosomal Protein
#1	dnaJ	35	Heat Shock Protein J
#2	pdhA/pdhB	36	(pyruvate) Oxoisovalerate Dehydrogenase Alpha & Beta Fusion
#3	aaaT	95	Neutral Amino Acid (Glutamate) Transporter
#4	pdhA	174	Pyruvate Dehydrogenase Alpha
#5	sucA	153	Oxoglutarate Dehydrogenase
#6	ycaH	197	ATPase
#7	glmU	74	UDP-GlcNAc Pyrophosphorylase
#8	tctD	196	HTH Transcriptional Regulatory Protein + Receiver Doman
#9	lpdA	300	Lipoamide Dehydrogenase
#10	tktB_1	232	Transketolase
#11	CPn1061	235	CT330 hypothetical protein
#12	xseA	130	Exodoxyribonuclease VII

Motif 1
TAAGAAGATTATTATTGTGTTTATAGAAGGCC	0	118	1
GGTGCATAGCATTTTTTTGTTTTTTCAACTGC	5	40	1
AAAAAAAATCTTTGTTTTTTTTCTGCAGTTGA	5	64	0
AAAACAAAGATTTTTTTTTTTTTGAAAAATAA	5	78	1
ACTTTTTTACTTTTTTCTTTTTTGAAAAATAG	8	105	0
TTCATAGCAAATTTTTATTTTTCAAAAAAAAA	5	92	0
    TACACCATTTTTCTTTTTGAGATCAAAT	6	6	1
TAATTATATTAGTTTTTTGTTTAACACAATTT	6	38	1
TTATATATATAGTGTTGTGTTTATGCAAAACT	8	75	1
CGGTAAATATTGTTTTCTTTTTTAATACCCAG	9	97	0
AATTCGTGAATTTCTTTTCTTTGGGTTTGAAT	3	36	0
TGTAATCCTTTTTGTTCTCTTTAAATTGCCAC	4	14	1
ATTCATATAATCTATTTTGTTTTCAT      	8	180	1
TTAAAAAAACTTAATTATTTTTTCTTCGGATA	4	75	1
TCGAAAAAATTTTAATATGTTTCTCGTGGCAA	4	39	0
TTAGATCGTATTTATTGAGTTTAATTATTTT 	5	132	1
TTGATCGAAAATTCATTTGTTTTTGAAAGAAT	10	128	1
TCGCTTCTAAATTATTAATTTTAAATTATATA	8	50	1
GCTGCCGTTGAGAGTTCTTTTTC         	10	1	0
AGGCCAGAGATTTGTTATTTATTGCGTAATAA	0	145	1
TAATATAAAATCAGTTATTTTTCAAAGGTCAC	8	141	0
          *** ** *****
MAP Score: 26.6204

Motif 2
TAAAATTTTTTCGATTTTTTAAAAAAACTTAATTATTTTTTCT	4	57	1
CAAAGATTTTTTTTTTTTTGAAAAATAAAAATTTGCTATGAAG	5	82	1
 TACACCATTTTTCTTTTTGAGATCAAATTAATTATATTAGTT	6	9	1
GGCGAAGATTGTGATCTTTTAAAAAGCATGATTTTCGTGCAAA	6	137	1
ATATATATAGTGTTGTGTTTATGCAAAACTATTTTTCAAAAAA	8	77	1
AAAAGTGTAAGTGACCTTTGAAAAATAACTGATTTTATATTAC	8	131	1
TAAATATTGTTTTCTTTTTTAATACCCAGAAGTATACTTGCAT	9	83	0
GAGGACCCTGTGCTTATTTTAGACCTAAAGATTAATTTTCAGC	9	198	0
CGTCTCTATCCCTAATTTTTAGTTAAAAAACTTTCCTGTTTAT	10	76	1
CTGTTTATTATTGAGATTTGATCGAAAATTCATTTGTTTTTGA	10	111	1
TTCCTATAGTTGCTGCTTTTACATAGAAGGTCTCCAGGGTTTA	10	196	1
TCATGAAAGTTCTCTCTTTGAGGAACAAGCTGTAGTTCGGTAG	11	198	1
TTAGAGTAAGTGATTTTCTGATAGAAAACTATTAAAAAATCAT	12	64	0
          *     *****   * **    *
MAP Score: 4.37071