AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile006_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243509
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	flhA	181	Flagellar Secretion Protein
#1	yscU	256	YopS Translocation Protein U
#2	CT552	300	hypothetical protein
#3	fmu	124	RNA Methyltransferase
#4	brnQ	149	Amino Acid (Branched) Transport
#5	CT555	174	SWI/SNF family helicase
#6	CT556	177	hypothetical protein
#7	lpdA	208	Lipoamide Dehydrogenase
#8	yscJ	103	Yop Translocation J
#9	yscL	275	Yop Translocation L
#10	uvrD	80	DNA Helicase

Motif 1
ACTAATCTTTTCTTTTTCCTTCTGGAGTCC	0	11	0
  TTACAGTATCTTTCTCTTGTCTAGTATA	0	163	0
AAGTTGTACAGCTTTTTCTTAAGGCTAACA	1	18	1
CTTTAGAATTTCTTTTTCCTTAATAATAAA	1	55	0
CACTAATCTTGCTTTTTCTTTAGAATTTCT	1	72	0
GAGAACGGAATATTTTTTTTAAAGAGCGTT	1	112	0
GCATCTGCCACCTTCTTTCTTGAGAAAAAC	1	179	1
GCACGAGGTTGCTTTTTCCTACGATAGATC	2	113	0
TTTTTCTAACCCTTTTTTCTCTTAACTCTC	2	152	1
CTTTTTTTCCGCTTTTTTCTAAGATTTCCT	2	204	1
TTAGAGAAAGTCTTTTTTCCTGTCCCGTTC	2	239	1
TTTCCTGTCCCGTTCTTTCTCAAGAGCTTT	2	254	1
CTACACGGTTGCTTTCTCCTATTGGGGAAG	3	58	0
GGCTAACGGACGTTTCTTCTAATTCATCCT	4	52	1
TCTAATTCATCCTTTATTCTTTCCAAAGAA	4	69	1
AAAGGTCAATCATTTCTTTTT         	6	1	0
GACCTTTTATTCTTCTTTTTACGTATTACC	6	24	1
GTATTACCTTGATTTTTTCCTCCTAGGAAC	6	46	1
CTTACGTTCCTATTTTTTCTCTCCTGCTAC	7	14	1
CAATCGGGAACATTTTTTCTGCAGAGAATG	8	34	0
ATTTGGTGCTTCTTTTTTTTGTATATATGG	9	42	0
TAGCATTGTAGATTTTTTCTCCGATGGCTA	9	71	1
ACAAGGATCGCATTCTTTTTTACACAGAGA	9	141	0
          **********
MAP Score: 30.8296

Motif 2
GGAAGGAGAATCCTCTTCCCTCAGATAATCATCT	7	138	1
ATTCATCCTTTATTCTTTCCAAAGAACTTCTGTG	4	73	1
GCACTAATCTTGCTTTTTCTTTAGAATTTCTTTT	1	69	0
AGGATCGCATTCTTTTTTACACAGAGATCGAGGT	9	134	0
GAGAACGGAATATTTTTTTTAAAGAGCGTTTTTC	1	108	0
ACTTTTTTTCCGCTTTTTTCTAAGATTTCCTGGT	2	203	1
TTTCCTGTCCCGTTCTTTCTCAAGAGCTTTTGTT	2	254	1
GCATCTGCCACCTTCTTTCTTGAGAAAAACATTT	1	179	1
CAATCGGGAACATTTTTTCTGCAGAGAATGCTTC	8	30	0
AGGACCTCTCTTTTCCTTTCCTAGAAAGGCTTGG	7	106	1
AAGAACCCCTTACTCTTTGTTTATAAATGGGATG	1	144	1
CTGCTACCACTTCTCCTCATTGAGATTTTATCCA	7	37	1
CCTTTTATTCTTCTTTTTACGTATTACCTTGATT	6	26	1
AATCTTTTCTTTTTCCTTCTGGAGTCCT      	0	4	0
AAACACTCGTTCCTTTCTGCCTAGGTCATGCGCA	5	120	1
CGATAGTTTATTCTCTTCCCCAATAGGAGAAAGC	3	44	1
TTTTAAAGAGCGTTTTTCATGAAGCACTAATCTT	1	92	0
GTTCTTATCCTACTCTTTGTTTGGATCTATCGTA	2	90	1
CGCACGAGGTTGCTTTTTCCTACGATAGATCCAA	2	110	0
TTGGTGCTTCTTTTTTTTGTATATATGGGAGTGT	9	36	0
    AACATTTCCTCTTCAATGAGTGTTTAGGAT	7	188	0
ATTACCTTGATTTTTTCCTCCTAGGAACTATAAT	6	48	1
GAAGTTGTACAGCTTTTTCTTAAGGCTAACACAG	1	17	1
CTTTAGAATTTCTTTTTCCTTAATAATAAAAAGG	1	51	0
ACTTGCGAAGTATTCCTTATAGCGCTTAAGCAAC	1	223	1
CCACATAACCTGTTCATTTTGAAGCATTCTCTGC	8	10	1
          * ****** *  **
MAP Score: 21.2261

Motif 3
TCTTTAAAAAAAATATTCCGTTCTCTAAAGAACC	1	117	1
CCGTTCTCTAAAGAACCCCTTACTCTTTGTTTAT	1	134	1
TTAAAGTAGGGAGGATATCGCTCTCTG       	2	3	0
GACTCATTAAAAGAATTCGTTGCTTTAAAGTAGG	2	27	0
ACCACTTATAGAACTTACGTTCTTATCCTACTCT	2	72	1
GCTTTTTTCTAAGATTTCCTGGTTGTTAGAGAAA	2	214	1
GTACTTTAAAGAGCATCCCTCTCTTGGCTCGAAG	3	92	1
TCTTTCCAAAGAACTTCTGTGACTTGGGAAGGAT	4	86	1
CCGGGCAAAAGAACATCCCTTACTTATTCAGTAA	5	42	0
AACGCCTTTAGAAGACACCTATCTACTCCTAAAC	5	90	1
ATCTACTCCTAAACACTCGTTCCTTTCTGCCTAG	5	110	1
          GAGATCACCTCTTTAACAGTCTTT	6	163	0
TATTTGTCTGAAGGACCTCTCTTTTCCTTTCCTA	7	95	1
    ATCAGGGAGATCTTCTCACTGCTATTACAC	9	6	1
CGAGGGTCAGGAAAACCTCGATCTCTGTGTAAAA	9	120	1
GCAAAGGAGCGAGGTTCCCTGCCTGTTGGCTTTG	9	224	1
GGCTTTGCCAAAGGATCCCTACCTCGTCAGAAGG	9	251	1
          *** ** ***  **
MAP Score: 16.6217

Motif 4
TTTAAATCGGAGTATAGCGCAGCCTGGTTAGCGCG	0	94	0
CTTTTTCTTAAGGCTAACACAGCCTTTTTATTATT	1	29	1
TCCGTTCTCTAAAGAACCCCTTACTCTTTGTTTAT	1	133	1
TAAAGTAGGGAGGATATCGCTCTCTG         	2	1	0
GATCTATCGTAGGAAAAAGCAACCTCGTGCGACAA	2	113	1
CTTCCCCAATAGGAGAAAGCAACCGTGTAGCTGCG	3	58	1
CGTACTTTAAAGAGCATCCCTCTCTTGGCTCGAAG	3	91	1
TACTTATAAGAGGGCATATCATCCTTCCCAAGTCA	4	105	0
CAATTGTTTGAAGCCATCCCTTACTGAATAAGTAA	5	22	1
TCCGGGCAAAAGAACATCCCTTACTTATTCAGTAA	5	42	0
AAACGCCTTTAGAAGACACCTATCTACTCCTAAAC	5	89	1
TGTTTGCAAGACGATACCCCTCCCGAATTATAGTT	6	73	0
GTAATAGCAGTGAGAAGATCTCCCTGAT       	9	3	0
TGGCTTTGCCAAAGGATCCCTACCTCGTCAGAAGG	9	250	1
          ***  * * ** ***
MAP Score: 12.3764

Motif 5
ATGAAAAACGCTCTTTAAAAAAAATATTCCGTTCTCTA	1	106	1
ATGCTCATCCCATTTATAAACAAAGAGTAAGGGGTTCT	1	145	0
CTGCCACCTTCTTTCTTGAGAAAAACATTTATATACGG	1	183	1
TCTCTTAACTCTCTATCTAAGAAATCTTTAGCGGACTT	2	169	1
GAAGAGAATAAACTATCGAGCAAAATGTAGAGATGATG	3	24	0
ATGATATGCCCTCTTATAAGTAAAAATTATCATTTTTT	4	118	1
CCTAAACACTCATTGAAGAGGAAATGTT          	7	190	1
TTGAAGCATTCTCTGCAGAAAAAATGTTCCCGATTGGC	8	28	1
AAACCTCGATCTCTGTGTAAAAAAGAATGCGATCCTTG	9	132	1
          ****    ** ***   *
MAP Score: 6.84