AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243344
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rl28	148	L28 Ribosomal Protein
#1	rl33	300	L33 Ribosomal Protein
#2	CT165	300	hypothetical protein
#3	CT167	55	hypothetical protein
#4	CT168	65	hypothetical protein
#5	trpR	55	Trp Operon Repressor
#6	dsbD	152	Thio:disulfide Interchange Protein
#7	amn	219	AMP Nucleosidase
#8	mrsA	245	Phosphoglucomutase
#9	tyrP_1	51	Tyrosine Transport

Motif 1
TTTTTTTATCAAAAAATCATTTTCTCACCGTGTC	1	87	1
TACGAAAACAAAAAAATCCCGCTCAAAAGCACCC	2	156	0
    AAAAACAAAAAAAATAAATCATTTAGTTTT	8	6	1
ACCTGTTAAAAACAAATCGTAATCACCAAAATTT	2	220	0
         AAACACAACACTCTCTCCGGTTTAG	6	137	0
TACCCTCACGAGAACAACTTGTTCCATCTTCATA	7	145	1
GAATTGCAAAAACAAAAACAACTCTTCTGTTGTT	6	93	1
CTATGTTTTTAGAAAAAAAGATTCTCTAACCATT	7	179	1
ATAAGAAGTAAGAAAATAATTATCGAAAACTAAA	8	31	0
GAATGTCGCGAAACAAACGCTTTCCCTCTTTCTT	7	75	1
TTTTTTGATAAAAAAATCCTTCTTCTCTTACACC	1	69	0
CTATTTTCAAAAATAATCAAGATCTGCTCTCGCA	1	228	0
ATTACTGGATAAAACAACTCTTTTTGCCTGGCAT	1	13	1
ATGTGTTTCAAAATAAAAGTACTCAAGGAAAC  	0	8	0
TTGGATTAGGAAAACTTCTTTATCAACTGGATTT	2	89	0
TGTTGCTACAAGAGAAAATTCCTCACAG      	2	282	1
ACTGTAACAAAAAGAAACTATGTTAGACCTTTTT	0	83	0
CCTTTGGCTCAAAACTAACTGATCCTTGATTTTC	8	201	0
AACAGGTAATAACAAATACCCGTTCCGAATCCGA	2	247	1
CTTGATTTTCAGAGATAAATATTCCCTATTTTTA	8	177	0
          ********    **
MAP Score: 14.0047

Motif 2
         GTTTCCTTGAGTACTTTTATTTT	0	1	1
CGGGAAGAAGTTTTCGTGAAAAAGTGGCAGAA	0	43	0
GAAAATGATTTTTTGATAAAAAAATCCTTCTT	1	79	0
GTATGTATAGTCTTATTAAAAAAGATATTGCT	1	136	1
GTTATGAGGGTCTCTTTGAATAAATGCGAGAG	1	204	1
AGATCTTGATTATTTTTGAAAATAGGTATAGC	1	237	1
TGATTTAGCATTTTCTTGAGAAAAGGTTCATT	1	277	1
TCCACTAAGGTTTTATTGAAATCCAGTTGATA	2	71	1
CCTAATCCAACCTTGTTGAAAACATCATAGAA	2	113	1
 TGTAGCATATATTTATGAAATGTTGTAATAT	5	9	1
AGAGAATCTTTTTTTCTAAAAACATAGTATGA	7	174	0
TTTTCTTACTTCTTATTTAAAAAGTGAATGGC	8	49	1
ATTGCAAAGATTTTGATAAAAATAGGGAATAT	8	161	1
AGGGAATATTTATCTCTGAAAATCAAGGATCA	8	184	1
     TGCTCTATCCCTAAGAATATCCTTTGG	8	228	0
GTTTTTTCTCTCTTGATGAATAGCATAAGCGT	9	18	1
          ****  ******
MAP Score: 13.6731

Motif 3
GGGAAGAAGTTTTCGTGAAAAAGTGGCAGAAAA	0	41	0
ATACTATGTTTTTAGAAAAAAAGATTCTCTAAC	7	176	1
GCTTTCCCTCTTTCTTGCAAAAGAAAACTATAC	7	93	1
      AGCATTGGGCGAAAAAGTCTCTAAGAA	4	4	1
TATGTATAGTCTTATTAAAAAAGATATTGCTAG	1	137	1
TTTCTTACTTCTTATTTAAAAAGTGAATGGCCG	8	50	1
AGGTAAGATCTTGGTTCAGAAAGTGCAACGTTA	1	175	1
GATCAGTTAGTTTTGAGCCAAAGGATATTCTTA	8	211	1
TCGCGACATTCTTCTGGACAAAGCTTAGAAGAG	7	53	0
TGCTCTCGCATTTATTCAAAGAGACCCTCATAA	1	205	0
GAAGGATTTTTTTATCAAAAAATCATTTTCTCA	1	81	1
ACAATGACATTTGCGGTCGAAAGTATGATTCCT	2	37	1
ATTGCAAAGATTTTGATAAAAATAGGGAATATT	8	161	1
ATCTTGATTATTTTTGAAAATAGGTATAGCATA	1	239	1
TAGCTTACTATTTATAACCAAACAAAAATTCAA	8	84	0
GATTTAGCATTTTCTTGAGAAAAGGTTCATTC 	1	278	1
TTCTTCCCGATATATTAAAAAAGGTCTAACATA	0	66	1
          *** *  ******
MAP Score: 11.3733

Motif 4
   GTTTCCTTGAGTACTTTTATTTTGAAACACATTTTCT	0	7	1
AAACACATTTTCTGCCACTTTTTCACGAAAACTTCTTCCC	0	34	1
GCGACCAGTATGTATAGTCTTATTAAAAAAGATATTGCTA	1	129	1
CGAGAGCAGATCTTGATTATTTTTGAAAATAGGTATAGCA	1	230	1
TAGGGGCTGATTTAGCATTTTCTTGAGAAAAGGTTCATTC	1	270	1
GAGCCACTTTTCTATGATGTTTTCAACAAGGTTGGATTAG	2	114	0
TGATGCTTCCTCTGTTTTCTACTCCTAAAATATGT     	3	5	0
          TGTAGCATATATTTATGAAATGTTGTAATA	5	0	1
AAACAAACGCTTTCCCTCTTTCTTGCAAAAGAAAACTATA	7	85	1
GTTCCATCTTCATACTATGTTTTTAGAAAAAAAGATTCTC	7	165	1
ATAATTATTTTCTTACTTCTTATTTAAAAAGTGAATGGCC	8	42	1
CAGAGATAAATATTCCCTATTTTTATCAAAATCTTTGCAA	8	162	0
          * *    * ** **   ***
MAP Score: 10.1747

Motif 5
TTTCTGCCACTTTTTCACGAAAACTTCTTCCCGAT	0	42	1
CGACAGGGCAACTGTAACAAAAAGAAACTATGTTA	0	92	0
AATTATTTGATGCCAGGCAAAAAGAGTTGTTTTAT	1	21	0
AGAAAATGATTTTTTGATAAAAAAATCCTTCTTCT	1	77	0
GTATGTATAGTCTTATTAAAAAAGATATTGCTAGA	1	136	1
TCAACAAGGTTGGATTAGGAAAACTTCTTTATCAA	2	97	0
TCCTAATCCAACCTTGTTGAAAACATCATAGAAAA	2	112	1
AAGCGGACAGAAAAATACGAAAACAAAAAAATCCC	2	170	0
TATTTGTTATTACCTGTTAAAAACAAATCGTAATC	2	230	0
ATCCGATTGTTGCTACAAGAGAAAATTCCTCACAG	2	275	1
  ACATATTTTAGGAGTAGAAAACAGAGGAAGCAT	3	8	1
TGGTATGTAATGAATTGCAAAAACAAAAACAACTC	6	82	1
AACGATAACATAGATGGAGAAAAGATAACGGGTTA	7	18	0
TCCCTCTTTCTTGCAAAAGAAAACTATACTTTTAA	7	97	1
CCCAACTATTACCCTCACGAGAACAACTTGTTCCA	7	136	1
CTTCATACTATGTTTTTAGAAAAAAAGATTCTCTA	7	172	1
AGTAAGAAAATAATTATCGAAAACTAAATGATTTA	8	24	0
ATGCTATTCATCAAGAGAGAAAAAACTGTAGATT 	9	9	0
          *   * * *******
MAP Score: 2.90877

Motif 6
AATGTGTTTCAAAATAAAAGTACTCAAGGAAAC 	0	9	0
GGGCAACTGTAACAAAAAGAAACTATGTTAGACC	0	88	0
TAAATTACTGGATAAAACAACTCTTTTTGCCTGG	1	10	1
CACCTAAAACGACAAATAATTATTTGATGCCAGG	1	39	0
ATGATTTTTTGATAAAAAAATCCTTCTTCTCTTA	1	73	0
TTTTTTATCAAAAAATCATTTTCTCACCGTGTCT	1	88	1
ATACGAAAACAAAAAAATCCCGCTCAAAAGCACC	2	157	0
AACAGGTAATAACAAATACCCGTTCCGAATCCGA	2	247	1
  AGCATTGGGCGAAAAAGTCTCTAAGAAGAGGA	4	8	1
TTCATTACATACCAAAAAGGATCTTGGTTCTATA	6	62	0
TGAATTGCAAAAACAAAAACAACTCTTCTGTTGT	6	92	1
        AAACACAACACTCTCTCCGGTTTAGC	6	136	0
GAAGAATGTCGCGAAACAAACGCTTTCCCTCTTT	7	72	1
TATGTTTTTAGAAAAAAAGATTCTCTAACCATTA	7	180	1
 AAAAACAAAAAAAATAAATCATTTAGTTTTCGA	8	9	1
GATTTTCAGAGATAAATATTCCCTATTTTTATCA	8	174	0
ATATCCTTTGGCTCAAAACTAACTGATCCTTGAT	8	205	0
        CTAAGATACAGACGCTTATGCTATTC	9	35	0
          ** *****  * **
MAP Score: 2.24835