AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons007_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237522
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	gcp_1	135	O-Sialoglycoprotein Endopeptidase
#1	rs21	178	S21 Ribosomal Protein
#2	dnaJ	35	Heat Shock Protein J
#3	pdhA/pdhB	36	(pyruvate) Oxoisovalerate Dehydrogenase Alpha & Beta Fusion
#4	aaaT	95	Neutral Amino Acid (Glutamate) Transporter
#5	pdhA	174	Pyruvate Dehydrogenase Alpha
#6	sucA	153	Oxoglutarate Dehydrogenase
#7	ycaH	197	ATPase
#8	ribC	255	Riboflavin Synthase
#9	glmU	74	UDP-GlcNAc Pyrophosphorylase
#10	tctD	196	HTH Transcriptional Regulatory Protein + Receiver Doman
#11	lpdA	300	Lipoamide Dehydrogenase
#12	tktB_1	232	Transketolase
#13	CPn1061	235	CT330 hypothetical protein
#14	xseA	130	Exodoxyribonuclease VII

Motif 1
TTTTTTAAAAAAACTTAATTATTTTTTCTTCGGATAGCCC	5	71	1
AAGGTCACTTACACTTTTTTACTTTTTTCTTTTTTGAAAA	10	109	0
CCCTCGGTAAATATTGTTTTCTTTTTTAATACCCAGAAGT	11	93	0
TTACAAGGTAAGAGTTCCTTGCTTTTTGCTTGGGGATTTC	12	159	1
CAAAAAAAAAAAAATCTTTGTTTTTTTTCTGCAGTTGAAA	6	62	0
TGACCTTTGAAAAATAACTGATTTTATATTACGTATTCAT	10	142	1
AATAAGTATAACAATTCGTGAATTTCTTTTCTTTGGGTTT	4	40	0
CAGTGACTTTAGAGTAAGTGATTTTCTGATAGAAAACTAT	14	75	0
CTTTCCCGACAGAATCAATGATTTTTTAATAGTTTTCTAT	14	47	1
ATAAATGTTTTCATTTCTTTCATTTTTATTTGATTAAAAG	0	61	1
GAGATCAAATTAATTATATTAGTTTTTTGTTTAACACAAT	7	28	1
GATTTGATCGAAAATTCATTTGTTTTTGAAAGAATTACAA	12	125	1
TTCCTAGAGTAGAGTATGTTTTTTTCGTCTCAATAAGCAA	8	186	0
CCATTATAGGAGAGTTCTTTATTTTCGTCTCTATCCCTAA	12	51	1
GTTTGTTGGTATAGTTTATTTTTTTATATCAAAAATCGAC	0	103	1
ATTCATTCATATAATCTATTTTGTTTTCAT          	10	176	1
ATGAAAACATTTATTGTTTTAATTTATTCAGATACATTAG	0	35	0
TTCTTCTGCAATACTAGCATTCTTTGTAATACGGCGAAGA	7	105	1
TAGATCGTATTTATTGAGTTTAATTATTTT          	6	133	1
CAGGTGCATAGCATTTTTTTGTTTTTTCAACTGCAGAAAA	6	38	1
GAAACATATTAAAATTTTTTCGATTTTTTAAAAAAACTTA	5	48	1
     GTGATGTAATCCTTTTTGTTCTCTTTAAATTGCCA	5	5	1
          * * *   **  *** *  *
MAP Score: 30.6892

Motif 2
GAAAACATTTATTGTTTTAATTTATTCAGATA	0	41	0
AAATGTTTTCATTTCTTTCATTTTTATTTGAT	0	63	1
GGTATAGTTTATTTTTTTATATCAAAAATCGA	0	110	1
TAAGAAGATTATTATTGTGTTTATAGAAGGCC	1	118	1
AGGCCAGAGATTTGTTATTTATTGCGTAATAA	1	145	1
CAATTCGTGAATTTCTTTTCTTTGGGTTTGAA	4	37	0
AAATTCACGAATTGTTATACTTATTTACCAAT	4	55	1
TGTAATCCTTTTTGTTCTCTTTAAATTGCCAC	5	14	1
TATTAAAATTTTTTCGATTTTTTAAAAAAACT	5	54	1
GGTGCATAGCATTTTTTTGTTTTTTCAACTGC	6	40	1
AAAAAAAATCTTTGTTTTTTTTCTGCAGTTGA	6	64	0
AAAAACAAAGATTTTTTTTTTTTTGAAAAATA	6	77	1
TTCATAGCAAATTTTTATTTTTCAAAAAAAAA	6	92	0
    TACACCATTTTTCTTTTTGAGATCAAAT	7	6	1
TAATTATATTAGTTTTTTGTTTAACACAATTT	7	38	1
TACGGCGAAGATTGTGATCTTTTAAAAAGCAT	7	134	1
TCTGTGCAAAATTGCTTTGCTTATTGAGACGA	8	170	1
      AGTAAGTTCTTTATATCTTGTAAGTA	9	4	1
TTATATATATAGTGTTGTGTTTATGCAAAACT	10	75	1
ACTTTTTTACTTTTTTCTTTTTTGAAAAATAG	10	105	0
CTCGGTAAATATTGTTTTCTTTTTTAATACCC	11	99	0
AATTTTCAGCATTGCTTTTTTCTTCGCTGATT	11	176	0
ATTATAGGAGAGTTCTTTATTTTCGTCTCTAT	12	53	1
TCACGGACTCTTTGCTCTACTTGTCGAATACG	13	151	0
GCGTCATGAAAGTTCTCTCTTTGAGGAACAAG	13	195	1
          ****** * ***
MAP Score: 28.3919

Motif 3
TCTGCAGTTGAAAAAACAAAAAAATGCTAT	6	45	0
AACTGCAGAAAAAAAACAAAGATTTTTTTT	6	66	1
TATATCCCAGAAAAAGCAAACGTTCCCTCG	11	127	0
TCAGCGAAGAAAAAAGCAATGCTGAAAATT	11	178	1
ATTGAGACGAAAAAAACATACTCTACTCTA	8	192	1
ATCCCCAAGCAAAAAGCAAGGAACTCTTAC	12	166	0
TGTGTTAAACAAAAAACTAATATAATTAAT	7	36	0
ACTATTTTTCAAAAAAGAAAAAAGTAAAAA	10	104	1
TCTGGGTATTAAAAAAGAAAACAATATTTA	11	96	1
CAAAGAAGTTAAAAAACTATGTCGCTTCTA	10	29	1
AAATATTTAGAAAATACAAA          	1	0	0
GTGATCTTTTAAAAAGCATGATTTTCGTGC	7	147	1
ATTTTTCAAAAAAAAAAAAATCTTTGTTTT	6	78	0
TTTTGATATAAAAAAATAAACTATACCAAC	0	107	0
CGATTTTTTAAAAAAACTTAATTATTTTTT	5	68	1
ATTTGATCTCAAAAAGAAAAATGGTGTA  	7	8	0
CTATCCGAAGAAAAAATAATTAAGTTTTTT	5	78	0
GTCCCCTTCGAAAATGCAATGCAACGACTA	13	22	1
ATTTTTAGTTAAAAAACTTTCCTGTTTATT	12	90	1
ATTTCCTAGAAAAAAACTTTGCAACTATAG	8	79	0
AGAAAAGATTAAAAATCAAGTTTACAAAGC	7	79	0
TAAAGAGAACAAAAAGGATTACATCAC   	5	7	0
AAAACTATTAAAAAATCATTGATTCTGTCG	14	53	0
TTAATCAAATAAAAATGAAAGAAATGAAAA	0	68	0
GCAACAATGTAAAAAATATTTAGAAAATAC	1	13	0
AAAAAACAAAAAAATGCTATGCACCTGCTC	6	35	0
TTTTTTTTTGAAAAATAAAAATTTGCTATG	6	92	1
          **********
MAP Score: 25.5755

Motif 4
      TTTGTATTTTCTAAATATTTTTTACA	1	4	1
TACAATCGAGGCTCTTCTAAAAGACATAGTAA	1	89	1
       AATTACATTATAAAATTTTGCTCGG	4	3	1
AAATTTTTTCGATTTTTTAAAAAAACTTAATT	5	59	1
GGATAGCCCTTGTCTTTTGAAACCTAGGCTCC	5	102	1
AAAGATTTTTTTTTTTTTGAAAAATAAAAATT	6	83	1
TACACCATTTTTCTTTTTGAGATCAAATTAAT	7	10	1
TTTTTAATCTTTTCTTCTGCAATACTAGCATT	7	94	1
AATACTAGCATTCTTTGTAATACGGCGAAGAT	7	114	1
ACGAAAATCATGCTTTTTAAAAGATCACAATC	7	143	0
ATATAGTGTTGTGTTTATGCAAAACTATTTTT	10	81	1
TTTACTTTTTTCTTTTTTGAAAAATAGTTTTG	10	100	0
TGAAGGGGGGTTCTTTTTGAAATCTTGATTAC	11	265	1
GAAAATTCATTTGTTTTTGAAAGAATTACAAG	12	134	1
CAGAATCAATGATTTTTTAATAGTTTTCTATC	14	56	1
TAGAGTAAGTGATTTTCTGATAGAAAACTATT	14	74	0
          * **** *****
MAP Score: 3.83157

Motif 5
AATGTTTTCATTTCTTTCATTTTTATTTGATTAAAA	0	64	1
AAATAACAAATCTCTGGCCTTCTATAAACACAATAA	1	129	0
TTTTCAAAGGTCACTTACACTTTTTTACTTTTTTCT	10	119	0
AATTATGAAATCACGACCTCTTAGGTCGCTAAAATG	11	41	1
GCTTTTTTCTTCGCTGATTCTGTATTGAACCTCGCC	11	159	0
        ATTCTCACTCACTGTAATCAAGATTTCA	11	282	0
TTTATTTTCGTCTCTATCCCTAATTTTTAGTTAAAA	12	68	1
AAGGTAAGAGTTCCTTGCTTTTTGCTTGGGGATTTC	12	163	1
TTTGGATGCATCTCTAGCCCTATATGAAGAAGCTGA	13	90	1
TTCTGCCAACTCACGGACTCTTTGCTCTACTTGTCG	13	157	0
         CTTCCTCTCCTTATTCTCTCTGAATTT	14	1	1
TATCAGAAAATCACTTACTCTAAAGTCACTGAATTC	14	84	1
          ** **  **** *  *
MAP Score: 1.56799