AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile007_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243559
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rpiA	94	Ribose-5-P Isomerase A
#1	CT214	300	hypothetical protein
#2	ribC	300	Riboflavin Synthase
#3	exbB	152	polysaccharide transporter
#4	mrsA	245	Phosphoglucomutase
#5	tyrP_1	51	Tyrosine Transport
#6	tyrP_2	181	Tyrosine Transport
#7	pssA	300	CDP-diacylglycerol-serine-O-phosphatidyltransferase

Motif 1
AATATGGTGAAAACCCAAAAAAGCGCAACACACT	1	27	1
TGATCTTTAGAACGGGGAAAAATCGCAGAGTCTT	1	209	0
AATAAAAATTAAAAAGAGAAAATAGTTTTT    	1	280	1
TATTAGGCGACTTTTGAAAAAAAATCACCACAAA	2	31	0
GCGGTTACTTATAATCAAAAAATAATTATACTCC	2	172	0
GAAAAACTAGATACACGAAAAAGCCCTCTCCGGA	2	223	0
CTTTTTAGCAATCTTGAAAAACTAGATACACGAA	2	238	0
GGTTTAGCAAATCATCAAACAACAGAAGAGTTGT	3	28	1
AATGAATTGCAAAAACAAAAACAACTCTTCTGTT	3	48	0
          AAAAACAAAAAAAATAAATCATTT	4	0	1
TAAGAAAATAATTATCGAAAACTAAATGATTTAT	4	23	0
CTTACTATTTATAACCAAACAAAAATTCAAACGG	4	80	0
TGCTATTCATCAAGAGAGAAAAAACTGTAGATT 	5	9	0
TCTATACTATATGGAGAAAAACAACTAGCAAACA	6	95	0
TTCCCCTATCAACATGAAAAAACAGGGGGAGGAG	6	156	1
ATTTCACTTGCTCAGGGAAAACACGCAATAACCA	7	26	1
GTTTTCGGCACTACACAGAAAACCCACAGATAGT	7	62	0
          **   ******* *
MAP Score: 11.2389

Motif 2
TTTTAAATATGGTGAAAACCCAAAAAAGCGC	1	22	1
TTATTTCGTAGGAGAAAACCTCAAGATAAAC	1	122	1
TCTTTAGAACGGGGAAAAATCGCAGAGTCTT	1	209	0
GACCGCCCGTAGAGAAAACCTTTCTAAGAAG	2	139	0
ATTCATCAAGAGAGAAAAAACTGTAGATT  	5	8	0
TATACTATATGGAGAAAAACAACTAGCAAAC	6	96	0
TCACTTGCTCAGGGAAAACACGCAATAACCA	7	29	1
TCGGCACTACACAGAAAACCCACAGATAGTT	7	61	0
TCTGTGTAGTGCCGAAAACATGTTCTGTGTA	7	77	1
          ** ********
MAP Score: 9.78242

Motif 3
     GTCTTGATAAAGCTTTGAAGGAATCTTGAAGAG	0	5	1
GAGGTTGTAGGATTACTGTTTGAGGAATAGAAGCCCTT	0	40	1
TCTCCTACGAAATAAATGTTTGCATGCTAAGAAAGATT	1	99	0
CACAATTCTTGATTGTGATTTGTGGTGATTTTTTTTCA	2	13	1
AAGATACCACGGTTTTTATTTTAATGGATAAAATCCTG	2	79	1
CTCGGAGTATAATTATTTTTTGATTATAAGTAACCGCT	2	169	1
GATTATAAGTAACCGCTGTTTGCCTTGATCAGATCCGG	2	190	1
ATAGAACCAAGATCCTTTTTGGTATGTAATGAATTGCA	3	71	0
AAAACTAAATGATTTATTTTTTTTGTTTTT        	4	2	0
TTTAGTTTTCGATAATTATTTTCTTACTTCTTATTTAA	4	31	1
TGGCCGTTTGAATTTTTGTTTGGTTATAAATAGTAAGC	4	77	1
TTGATACCCAGATTGATGTTTGAGGAAAGGTCTTAAGA	4	117	1
GCGACTGTTTGCTAGTTGTTTTTCTCCATATAGTATAG	6	90	1
AGTCAAAGGAGATGTATATTTGTTTGCATAAATGCAAA	7	183	1
AGTGGGGCTTAGTTTATTTTTTTGTTGAGAAGCTTCTT	7	234	0
          ***   * ****  *  *
MAP Score: 9.18732

Motif 4
         GTCTTGATAAAGCTTTGAAGG	0	1	1
CTTGATAAAGCTTTGAAGGAATCTTGAAGA	0	12	1
TTTGAAGGAATCTTGAAGAGGTTGTAGGAT	0	23	1
TAGGATTACTGTTTGAGGAATAGAAGCCCT	0	47	1
AGATTCTTTCCTTTGAGAGGTTT       	0	81	1
TAGTTAAGATCTTTGAGAAGGTGAGGTAAA	1	171	1
ATTAGGCGACTTTTGAAAAAAAATCACCAC	2	34	0
CTGTGTCTTGTGTTGAAAAGAACCTCTTCT	2	114	1
TTTTTAGCAATCTTGAAAAACTAGATACAC	2	241	0
CCAGATTGATGTTTGAGGAAAGGTCTTAAG	4	124	1
ATTGCAAAGATTTTGATAAAAATAGGGAAT	4	161	1
GTTTTTTCTCTCTTGATGAATAGCATAAGC	5	18	1
TGTTTTTTCATGTTGATAGGGGAATCTTTC	6	150	0
TTTATTTTTTTGTTGAGAAGCTTCTTTTTA	7	230	0
          **********
MAP Score: 8.16368

Motif 5
CTTCAAGATTCCTTCAAAGCTTTATCAAGAC   	0	7	0
TGTTTGCATGCTAAGAAAGATTTATAGACAATCT	1	87	0
TCTTTCTTAGCATGCAAACATTTATTTCGTAGGA	1	101	1
ACTAAAGACTCCAGGAAAGATCGTTTATCTTGAG	1	141	0
TTACCTCACCTTCTCAAAGATCTTAACTAAAGAC	1	166	0
AGAACCTCTTCTTAGAAAGGTTTTCTCTACGGGC	2	132	1
TTGTCACGACCTAGCAAAGGTATTTAATTGTCT 	2	277	1
CTAGACGATCCTAACAAATTTCTTGTATAGAACC	3	101	0
GATTGATGTTTGAGGAAAGGTCTTAAGAAGGCGA	4	127	1
AAGAAGGCGAATTGCAAAGATTTTGATAAAAATA	4	151	1
TTAGGCTTCACAAAGAAAGATGTAAAAAATATGC	7	116	1
CCTCAGGAATCGCGGAAATTTATTACAGAAATCA	7	271	0
          *  ****** * **
MAP Score: 7.92737

Motif 6
TTGCGCTTTTTTGGGTTTTCACCATATTTA	1	25	0
ATCGTTTATCTTGAGGTTTTCTCCTACGAA	1	126	0
GAAAGACTCTGCGATTTTTCCCCGTTCTAA	1	207	1
ATTTTCTCTTTTTAATTTTTATTCTGCACA	1	273	0
ATTCTTGATTGTGATTTGTGGTGATTTTTT	2	17	1
GTGATTTGTGGTGATTTTTTTTCAAAAGTC	2	27	1
TTTTCGTGTATCTAGTTTTTCAAGATTGCT	2	236	1
CAACAGAAGAGTTGTTTTTGTTTTTGCAAT	3	47	1
AACTAAATGATTTATTTTTTTTGTTTTT  	4	8	0
AAATAAATCATTTAGTTTTCGATAATTATT	4	21	1
GAATGGCCGTTTGAATTTTTGTTTGGTTAT	4	74	1
GATACCCAGATTGATGTTTGAGGAAAGGTC	4	119	1
TCAAGGATCAGTTAGTTTTGAGCCAAAGGA	4	206	1
CTGTTTGCTAGTTGTTTTTCTCCATATAGT	6	94	1
ATAACTATCTGTGGGTTTTCTGTGTAGTGC	7	59	1
TGGGGCTTAGTTTATTTTTTTGTTGAGAAG	7	240	0
          **********
MAP Score: 6.41495

Motif 7
GGTTGTAGGATTACTGTTTGAGGAATAGAAGCCCTTGT	0	42	1
CATGCAAACATTTATTTCGTAGGAGAAAACCTCAAGAT	1	111	1
GTGATTTGTGGTGATTTTTTTTCAAAAGTCGCCTAATA	2	27	1
TACCACGGTTTTTATTTTAATGGATAAAATCCTGTGTC	2	83	1
CGGAGTATAATTATTTTTTGATTATAAGTAACCGCTGT	2	171	1
AAAAAGGATCTTGGTTCTATACAAGAAATTTGTTAGGA	3	89	1
AATTATTTTCTTACTTCTTATTTAAAAAGTGAATGGCC	4	44	1
GCCGTTTGAATTTTTGTTTGGTTATAAATAGTAAGCTA	4	79	1
GATACCCAGATTGATGTTTGAGGAAAGGTCTTAAGAAG	4	119	1
TAACTGATCCTTGATTTTCAGAGATAAATATTCCCTAT	4	182	0
CAAGGATCAGTTAGTTTTGAGCCAAAGGATATTCTTAG	4	207	1
GGGCTTAGTTTATTTTTTTGTTGAGAAGCTTCTTTTTA	7	230	0
          **  ****     * ***
MAP Score: 4.50639

Motif 8
GTGTTGCGCTTTTTTGGGTTTTCACCATATTT	1	26	0
AATGAAAGACTCTGCGATTTTTCCCCGTTCTA	1	204	1
  AAAAACTATTTTCTCTTTTTAATTTTTATT	1	280	0
ACAGAAGAGTTGTTTTTGTTTTTGCAATTCAT	3	49	1
ATGATTTATTTTTTTTGTTTTT          	4	0	0
AAAAAATAAATCATTTAGTTTTCGATAATTAT	4	18	1
AAATCAAGGATCAGTTAGTTTTGAGCCAAAGG	4	203	1
AGATTTCCTTTATGCGAGCTTTTTGTAAACAG	6	41	1
AGCGCGACTGTTTGCTAGTTGTTTTTCTCCAT	6	87	1
AGTTATGGTTATTGCGTGTTTTCCCTGAGCAA	7	33	0
ACCATAACTATCTGTGGGTTTTCTGTGTAGTG	7	56	1
ATGTAAAAAATATGCGCTGTTTAGTCCTTTTG	7	135	1
          * **** *****
MAP Score: 3.86099

Motif 9
GACATGGCAGATTGTCTATAAATCTTTCTTAGCA	1	79	1
TTAGGCGACTTTTGAAAAAAAATCACCACAAATC	2	29	0
ATAATTATTTTTTGATTATAAGTAACCGCTGTTT	2	177	1
GTTTTTCAAGATTGCTAAAAAGTATTGTTGTCAC	2	250	1
TGAATTTTTGTTTGGTTATAAATAGTAAGCTATT	4	85	1
CAGATTGATGTTTGAGGAAAGGTCTTAAGAAGGC	4	125	1
ATTGCAAAGATTTTGATAAAAATAGGGAATATTT	4	161	1
ATGCGAGCTTTTTGTAAACAGATCGAAATGATGA	6	52	1
AATTTGCATTTATGCAAACAAATATACATCTCCT	7	189	0
          ****   * *****
MAP Score: 3.55411

Motif 10
       GTCTTGATAAAGCTTTGAAGGAATCTT	0	3	1
TGACGGAGAGTGTGTTGCGCTTTTTTGGGTTTTC	1	35	0
AAAGATCGTTTATCTTGAGGTTTTCTCCTACGAA	1	126	0
CTATTTTCTCTTTTTAATTTTTATTCTGCACACA	1	271	0
AACACAATTCTTGATTGTGATTTGTGGTGATTTT	2	11	1
GATAAAATCCTGTGTCTTGTGTTGAAAAGAACCT	2	105	1
GGCTTTTTCGTGTATCTAGTTTTTCAAGATTGCT	2	232	1
ACTCTTCTGTTGTTTGATGATTTGCTAAACCGGA	3	25	0
AACAGAAGAGTTGTTTTTGTTTTTGCAATTCATT	3	48	1
AAATGATTTATTTTTTTTGTTTTT          	4	0	0
GCGCGACTGTTTGCTAGTTGTTTTTCTCCATATA	6	88	1
TAACCATAACTATCTGTGGGTTTTCTGTGTAGTG	7	54	1
AAATATGCGCTGTTTAGTCCTTTTGGCACTAGAA	7	142	1
TCAAAGGAGATGTATATTTGTTTGCATAAATGCA	7	185	1
          *** * * * ****
MAP Score: 1.62533