AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_fusions002_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236801
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	glnP	48	ABC Amino Acid Transporter Permease
#1	argR	83	Arginine Repressor
#2	oppB_1	292	Oligopeptide Permease
#3	oppC_1	30	Oligopeptide Permease
#4	tauB	271	ABC Transport ATPase (Nitrate/Fe)
#5	CPn0249	57	CT151 hypothetical protein
#6	ytgA	300	Solute Protein Binding Family
#7	accA	74	AcCoA Carboxylase/Transferase Alpha
#8	CPn0415	55	CT266 hypothetical protein
#9	himD	300	Integration Host Factor Alpha
#10	dppD	54	ABC ATPase Dipeptide Transport

Motif 1
 AAAAAACCAAGAAAAGAAAACGTTGCCTTTTAT	1	9	1
AATTTTGTTAAGAAACAAAAAGATCCTGAGAGGA	6	53	0
TTGTTTTATAAGAAAACAAAATGTTATAGAAAAA	6	118	0
TCCGAAATGGAAAAATTAAAAATTTTATAGACAA	2	11	1
TATCTTGAATAGAAACGAAGGCTTGCGGTTACCA	4	236	0
GCAATTGTTAAAAAAATAAGAGATTTATAGAAAA	2	143	1
GAAGATGACTAAAAATGAAAGTATAATGACTTAA	2	212	1
AGATTTATAGAAAAATAAAAGTCTTCCTTCCCAA	2	163	1
TCTCAATATGAGCAAGTAAAAGTTACATGGGGTT	1	56	1
TCTTGAAAAGAGAATTAAAAATTTTTAATTTAAA	2	45	1
GTTTCTTAACAAAATTCAAAACATAAAAATCGTA	6	71	1
  AAGTCATAAGAAAAAAAGAAGCATAAACTT  	3	8	1
AAAATCGTAAAGTAAAGAAGATTTTTTCTATAAC	6	96	1
ATTTAAGCTCAACAAAGAAAGTATAGGAAAATCT	4	14	0
CCCAATAAGGGAAAAGTAAAGAATCATCTTACCT	4	56	0
ACAACTAATAGAAATGAAAGAAATATCTTTGTTC	6	183	0
AAAATATTGCAAAAAGGAGAACTTGCAATATAAT	6	19	0
          *****  ****  *
MAP Score: 18.778

Motif 2
TGCATAAATATGATTTCATTATAAATAAATATGCAT	0	11	1
ATTGCAACTATAATTTAAATTAAAAATTTTTAATTC	2	56	0
ATTTAAATTATAGTTGCAATTGAAAACGCCCCTAAG	2	72	1
TATAAATCTCTTATTTTTTTAACAATTGCATTTCAC	2	136	0
AGGAAGACTTTTATTTTTCTATAAATCTCTTATTTT	2	155	0
TCCCAACGCATTTTTTGTATTGAAGATGACTAAAAA	2	191	1
TAAGTCATTATACTTTCATTTTTAGTCATCTTCAAT	2	209	0
TTTATGCTTCTTTTTTTCTTATGACTT         	3	1	0
GTAGAGCGTCTGATTTGCATTCAGAAGGTCAGGAGT	4	114	1
CCGCAAGCCTTCGTTTCTATTCAAGATAGAGGCTTT	4	242	1
ACGATTTTTATGTTTTGAATTTTGTTAAGAAACAAA	6	68	0
AGAAAAAATCTTCTTTACTTTACGATTTTTATGTTT	6	89	0
GTAAAGAAGATTTTTTCTATAACATTTTGTTTTCTT	6	107	1
CTATAACATTTTGTTTTCTTATAAAACAAACGGGTT	6	123	1
ACGGGTTTTCTAATTTTTTTAAAACTATCCTGAACA	6	152	1
ACAAAGATATTTCTTTCATTTCTATTAGTTGTATTT	6	185	1
GGATAAAATATATTTTGAATAGAACTTGTTTTTCTG	6	227	1
TGTTTAAGAATTGTTTGTATTAAAATGATTCTTTTT	7	27	1
TATCTATTCATCCTTTGGATTCAAGACATTTTTTAA	9	189	0
          *  ***  *** ** *
MAP Score: 14.737

Motif 3
          AAAAAACCAAGAAAAGAAAACG	1	0	1
TCCGAAATGGAAAAATTAAAAATTTTATAGAC	2	11	1
ATCTTGAAAAGAGAATTAAAAATTTTTAATTT	2	44	1
TGCAATTGTTAAAAAAATAAGAGATTTATAGA	2	142	1
AGATTTATAGAAAAATAAAAGTCTTCCTTCCC	2	163	1
GAAGATGACTAAAAATGAAAGTATAATGACTT	2	212	1
   AAGTCATAAGAAAAAAAGAAGCATAAACT	3	7	1
ATTTAAGCTCAACAAAGAAAGTATAGGAAAAT	4	16	0
CCCAATAAGGGAAAAGTAAAGAATCATCTTAC	4	58	0
ATTTTGTTAAGAAACAAAAAGATCCTGAGAGG	6	54	0
AACAAAATTCAAAACATAAAAATCGTAAAGTA	6	78	1
CATAAAAATCGTAAAGTAAAGAAGATTTTTTC	6	92	1
TTTGTTTTATAAGAAAACAAAATGTTATAGAA	6	121	0
TACAACTAATAGAAATGAAAGAAATATCTTTG	6	186	0
TTAAAGTACCAGAAAAACAAGTTCTATTCAAA	6	240	0
TGAGACAAAGAAGACTACAAGAA         	8	1	0
CTGAGCTACGAGGACGCAAAGACCAGCACTTT	9	11	1
          *****  *****
MAP Score: 13.6875

Motif 4
CTTTTCAAGATTGTCTATAAAATTTTTAATTTTTC	2	20	0
CAACTATAATTTAAATTAAAAATTTTTAATTCTCT	2	53	0
AAATCTCTTATTTTTTTAACAATTGCATTTCACGT	2	134	0
TTTAGTCATCTTCAATACAAAAAATGCGTTGGGAA	2	190	0
AAGCCTTCGTTTCTATTCAAGATAGAGGCTTTTCC	4	246	1
AAAAATCTTCTTTACTTTACGATTTTTATGTTTTG	6	87	0
AAAGAAGATTTTTTCTATAACATTTTGTTTTCTTA	6	109	1
GGTTTTCTAATTTTTTTAAAACTATCCTGAACAAA	6	155	1
GAAAAACAAGTTCTATTCAAAATATATTTTATCCA	6	226	0
GGGTCTGTAATTGTGTTTAAGAATTGTTTGTATTA	7	14	1
CTTTACCAAGTTAGATTAAAGAAGTCACGTGTTAG	9	39	1
TTAGGGGAAGTTTTTCTCAAGATGTGGGAATGATT	9	89	1
TGATTGCGCATTTTTTAAAAAATGTCTTGAATCCA	9	175	1
CAATAATAACTTGCCTAAACGATCTTGTAAACGAC	10	27	1
          **   ** ***** *
MAP Score: 9.7876

Motif 5
GAAATGGAAAAATTAAAAATTTTATAGACAATC	2	14	1
TTGAAAAGAGAATTAAAAATTTTTAATTTAAAT	2	47	1
GCCCCTAACTACTGAATCTACGTGAAATGCAAT	2	115	1
ATTGTTAAAAAAATAAGAGATTTATAGAAAAAT	2	146	1
ATTTATAGAAAAATAAAAGTCTTCCTTCCCAAC	2	165	1
AAGTATAATGACTTAAACATTTTAGAGCTGAGG	2	230	1
AGGGAAAAGTAAAGAATCATCTTACCTATCAAG	4	50	0
AAAATTCAAAACATAAAAATCGTAAAGTAAAGA	6	81	1
ATCGTAAAGTAAAGAAGATTTTTTCTATAACAT	6	99	1
AATAGAAATGAAAGAAATATCTTTGTTCAGGAT	6	178	0
CCTCGTATAAAAAGAATCATTTTAATACAAACA	7	38	0
AAGTTAGATTAAAGAAGTCACGTGTTAGATGCA	9	46	1
GAGTAACCGTAAATAATAAACTTTTGAAGTCTA	9	234	0
          ******   ****
MAP Score: 9.63921

Motif 6
AATGGAAAAATTAAAAATTTTATAGACAAT	2	16	1
GAAAAGAGAATTAAAAATTTTTAATTTAAA	2	49	1
TCTTATTTTTTTAACAATTGCATTTCACGT	2	134	0
GTATAATGACTTAAACATTTTAGAGCTGAG	2	232	1
GACAACCCTATTAAGCATTTCTACCTTGAA	2	268	0
TTTTTGTTTCTTAACAAAATTCAAAACATA	6	66	1
AGGATAGTTTTAAAAAAATTAGAAAACCCG	6	153	0
TTAATGGATCTTAAAAAATGCTTCTAGAGA	6	279	1
GTAATTGTGTTTAAGAATTGTTTGTATTAA	7	20	1
AAGACATTTTTTAAAAAATGCGCAATCACT	9	173	0
          **********
MAP Score: 5.84741

Motif 7
TTTTCAAGATTGTCTATAAAATTTTTAATTTTTCCATTTCGGA	2	11	0
ATAGAACTTGTTTTTCTGGTACTTTAAGTGGTTTTTAATGGAT	6	245	1
TGAACAAAGATATTTCTTTCATTTCTATTAGTTGTATTTCTTG	6	182	1
GGTCTGTAATTGTGTTTAAGAATTGTTTGTATTAAAATGATTC	7	15	1
AAGAAGATTTTTTCTATAACATTTTGTTTTCTTATAAAACAAA	6	110	1
CTTGTAGTCTTCTTTGTCTCAGTTGTTAGAGTCAGACCGGTTT	8	12	1
TCCTATACTTTCTTTGTTGAGCTTAAATCTCTTGATAGGTAAG	4	20	1
CAAGCCTTCGTTTCTATTCAAGATAGAGGCTTTTCC       	4	245	1
AAAATCTTCTTTACTTTACGATTTTTATGTTTTGAATTTTGTT	6	78	0
CGAATAACTATATTTCTAGAACCTAGAAAAATCATTCCCACAT	9	110	0
AAATCTCTTATTTTTTTAACAATTGCATTTCACGTAGATTCAG	2	126	0
AAAAACCCCATGTAACTTTTACTTGCTCATATTGAGAAGTCCC	1	50	0
GTTTAAGTCATTATACTTTCATTTTTAGTCATCTTCAATACAA	2	205	0
GCAACTATAATTTAAATTAAAAATTTTTAATTCTCTTTTCAAG	2	46	0
          * * * *   * **  *    **
MAP Score: 5.54286

Motif 8
GGAAAAGCCTCTATCTTGAATAGAAACGAA	4	251	0
TTTTTTAAAACTATCCTGAACAAAGATATT	6	166	1
TTAAGCATTTCTACCTTGAAGTAGACCTCA	2	258	0
ATTTTATAGACAATCTTGAAAAGAGAATTA	2	32	1
TTTTTAAAAAATGTCTTGAATCCAAAGGAT	9	186	1
          CTCTCTAGAAGCATTTTTTA	6	290	0
CTTGCCTAAACGATCTTGTAAACGACTT  	10	36	1
TGGATAAAATATATTTTGAATAGAACTTGT	6	226	1
TACGATTTTTATGTTTTGAATTTTGTTAAG	6	75	0
TTGAGCTTAAATCTCTTGATAGGTAAGATG	4	36	1
GAATAACTATATTTCTAGAACCTAGAAAAA	9	122	0
GTAAATAATAAACTTTTGAAGTCTAAGCTC	9	229	0
          **********
MAP Score: 3.96891

Motif 9
TTAGGGGCCCCGATTCTTAGGGGCGTTTTCAATT	2	89	0
CACGTAGATTCAGTAGTTAGGGGCCCCGATTCTT	2	105	0
ACGTGAAATGCAATTGTTAAAAAAATAAGAGATT	2	134	1
TTCAGAAGGTCAGGAGTTCGAATCTCCTAGTCTC	4	133	1
TCTCTAGAAGCATTTTTTAAGATCCATTAAAAAC	6	275	0
TTAATACAAACAATTCTTAAACACAATTACAGAC	7	16	0
TTCTTTGTCTCAGTTGTTAGAGTCAGACCGGTTT	8	21	1
TTAAAGAAGTCACGTGTTAGATGCACGCTAGCAA	9	54	1
AGTGATTGCGCATTTTTTAAAAAATGTCTTGAAT	9	173	1
          ** ** *****  *
MAP Score: 2.76713

Motif 10
TGTCTATAAAATTTTTAATTTTTCCATTTCG	2	13	0
AGAATTAAAAATTTTTAATTTAAATTATAGT	2	55	1
TTCCCAACGCATTTTTTGTATTGAAGATGAC	2	190	1
TTATACTTTCATTTTTAGTCATCTTCAATAC	2	207	0
TTATGCTTCTTTTTTTCTTATGACTT     	3	5	0
GGTAAGATGATTCTTTACTTTTCCCTTATTG	4	57	1
TTTTTGCAATATTTTTCCTCTCAGGATCTTT	6	38	1
AGAAAAAATCTTCTTTACTTTACGATTTTTA	6	94	0
AGTAAAGAAGATTTTTTCTATAACATTTTGT	6	106	1
TATAACATTTTGTTTTCTTATAAAACAAACG	6	124	1
ACAAAGATATTTCTTTCATTTCTATTAGTTG	6	185	1
GTGTTTAAGAATTGTTTGTATTAAAATGATT	7	26	1
AACACGTGACTTCTTTAATCTAACTTGGTAA	9	41	0
          ******* ***
MAP Score: 1.55589