AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons018_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242674
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	tpiS	196	Triosephosphate Isomerase
#1	CT330	208	hypothetical protein
#2	pykF	96	Pyruvate Kinase
#3	uvrA	22	Excinuclease ABC Subunit A
#4	proS	200	Prolyl tRNA Synthetase
#5	thrS	229	Threonyl tRNA Synthetase
#6	minD	300	chromosome partitioning ATPase-CHLTR plasmid protein homolog GP5D
#7	trpS	198	Tryptophanyl tRNA Synthetase
#8	uvrB	24	Exinuclease ABC Subunit B
#9	CT684	300	ABC Transporter
#10	parB	135	Chromosome Partitioning Protein

Motif 1
ATTTTTATATGATTTATTTTCTATTGCTTTGA	0	95	0
ATTACGCTTTGATCTATCTTACAAAATACATG	0	152	1
GTCTTCAAAAGAGATTTTTTCCACGTTT    	1	6	0
TTAATAACTTGATGTTTCTTTTGTTTGTTTCT	4	55	0
TTAACTATACGATTTTTCTTCCCATGGTAGTT	6	44	1
GGTATCTGGAGAGCTTTCTTACTTTATTCATC	6	168	1
TAAAAATCCAGAGATGTCTTGCATCGATAAAT	7	109	1
AGCAAGGAGCGAGGTTTTTTCCCAAACAGGGT	7	157	1
AGAAAAATTCCATTTTTTTTACGATTCGTAGC	9	47	1
TGCAATTCGAGATATTTTTTTCGAACACCTTC	9	175	0
TGCAGTTCAGGATTTGTTTTGCCTTTTTTGAG	9	203	1
          *** ****** *
MAP Score: 15.8477

Motif 2
TGCAAGGAAGGCTTATTTTTATATGATTTATTTTC	0	106	0
GTCTTTAGAAGCTTCTCTTGCCTTGTATGAAGAGG	1	88	1
ATAGTTGAAGGCTTCTTTCATTTCGGATATTCTAG	2	35	1
CTATTGTAGGGCATCTCTTGAAAAAAACCCAGGTT	5	90	1
GTTCGGAGGAGCTTCTTTTAGGAGATTGTATAGAG	5	146	0
AGGAAGCCTCGCTCCTTTTTAGTTGCTTTAATTCC	6	245	0
TTCCTAACAATCATCTTTCTAAAGATGATGTTACA	7	20	1
GGCTTTAGGGGCTTATTTTTCGTAAAAATCCAGAG	7	87	1
GGGAGAGACATCCTCTTTCCCTAGGCTGTCTTTCT	9	129	1
AGGCTGTCTTTCTTTTTTTTTCAAGAAGGTGTTCG	9	151	1
GATTTGTTTTGCCTTTTTTGAGACAGAGGAGATAA	9	213	1
GGAGATAATAGGCTCTTTTCTCACGAGCTCCACTC	9	240	1
     GATCCTCCTCTTTCATCAGGATGCCACTCT	9	280	0
TGCCCACTCCGCATCTCTCTTGACAACAGAAGCGT	10	11	0
TGCGGAGTGGGCATCTCTTGATTTGCATTATAAGA	10	33	1
          ** ******   * *
MAP Score: 14.4808

Motif 3
AAGCAAATTCACAGAAAAAAGTAAGACAAGAAGATT	0	38	1
ATCAAAGCAATAGAAAATAAATCATATAAAAATAAG	0	94	1
TCATAGACCTTATGAATCAACCAACCACGTCTTTAG	1	60	1
GAATATCCGAAATGAAAGAAGCCTTCAACTATACAA	2	31	0
AAATTAATTTTAAGAAACAAACAAAAGAAACATCAA	4	43	1
ATCAAGTTATTAAGAAATAAAGAATCTGAACTAGTT	4	74	1
TAAAATCCAATAAGAACAAAAAAATCACAGAGATTG	4	109	1
CGATCCGTTCTATAGAACAACCAAGCTTGTTGCTAG	5	31	1
GTAGCGTTTCACGGAACTAAGCAAAAGGGTTTTATA	5	202	0
AAAGGAGATGAATAAAGTAAGAAAGCTCTCCAGATA	6	170	0
CGTCCATGCTTATGGACAAATCAATATAAAGGAATT	6	215	1
AATCAATATAAAGGAATTAAAGCAACTAAAAAGGAG	6	233	1
ATCGATAAATTAAGAATTAAAGAAAAAGCAAGGAGC	7	131	1
ACAAACAAATAAAAAATCAAAAAATCGCTAGA    	9	6	0
CTTCTTGAAAAAAAAAGAAAGACAGCCTAGGGAAAG	9	143	0
          ** ***  **  ** *
MAP Score: 13.4231

Motif 4
GCTAATCTTCTTGTCTTACTTTTTTCTGTGAATTT	0	42	0
CTTTAGAAGCTTCTCTTGCCTTGTATGAAGAGGCT	1	90	1
TGTTTAATACGTGCTTCGACTTCTTGAATGCGAGA	1	149	0
TAACTTGATGTTTCTTTTGTTTGTTTCTTAAAATT	4	48	0
AACTAGTTCAGATTCTTTATTTCTTAATAACTTGA	4	75	0
CAATCTCTGTGATTTTTTTGTTCTTATTGGATTTT	4	110	0
AGGGAAGGAAGTGCTTTATATTGTTTCGTGTGGAA	4	175	0
CCCTACAATAGATCCTTATTTTTTTAGTGCACAGC	5	66	0
ATCTGGAGAGCTTTCTTACTTTATTCATCTCCTTT	6	171	1
GCTCCTTGCTTTTTCTTTAATTCTTAATTTATCGA	7	132	0
    TCTAGCGATTTTTTGATTTTTTATTTGTTTG	9	6	1
TTTCCCTAGGCTGTCTTTCTTTTTTTTTCAAGAAG	9	144	1
AGTTCAGGATTTGTTTTGCCTTTTTTGAGACAGAG	9	206	1
ATAAGATTTTGTATCTTGAGTTTTTGTATTCTGGG	10	62	1
          ** ****   ** **
MAP Score: 12.6696

Motif 5
AGATTAGCATATCCAAGAGATTTATATCAA	0	69	1
TAAGCCTTCCTTGCAAGAAATCGAGTATTA	0	126	1
AAAAATCTCTTTTGAAGACGCTATGAAACG	1	19	1
TATGAAACGTTTGGAAGAGATCATAGACCT	1	40	1
TCTTCATACAAGGCAAGAGAAGCTTCTAAA	1	91	0
TCTTGCCTTGTATGAAGAGGCTGATCAATT	1	103	1
TGAGTCTCGCATTCAAGAAGTCGAAGCACG	1	145	1
AATATCCGAAATGAAAGAAGCCTTCAACTA	2	36	0
CCTGGGTTTTTTTCAAGAGATGCCCTACAA	5	93	0
GCAACTACCATGGGAAGAAAAATCGTATAG	6	48	0
TAATTTATCGATGCAAGACATCTCTGGATT	7	113	0
TAAATTAAGAATTAAAGAAAAAGCAAGGAG	7	136	1
TTGAAAAAAAAAGAAAGACAGCCTAGGGAA	9	145	0
TTTCTTTTTTTTTCAAGAAGGTGTTCGAAA	9	159	1
TGGCATCCTGATGAAAGAGGAGGATC    	9	284	1
ACGCTTCTGTTGTCAAGAGAGATGCGGAGT	10	11	1
TTATAATGCAAATCAAGAGATGCCCACTCC	10	36	0
          **********
MAP Score: 11.2674

Motif 6
CAAACAGCCCTTAAGAAAAAAACTTGTTGGCT	9	76	0
GTAGGGCATCTCTTGAAAAAAACCCAGGTTGA	5	95	1
TCGAACACCTTCTTGAAAAAAAAAGAAAGACA	9	155	0
CGGGACCCTGTTTGGGAAAAAACCTCGCTCCT	7	161	0
TGGCTACGAATCGTAAAAAAAATGGAATTTTT	9	49	0
CTCTGGATTTTTACGAAAAATAAGCCCCTAAA	7	90	0
TAAATTAATTTTAAGAAACAAACAAAAGAAAC	4	42	1
        AAACGTGGAAAAAATCTCTTTTGA	1	2	1
TTAAGCAAATTCACAGAAAAAAGTAAGACAAG	0	36	1
AAGAAGGTGTTCGAAAAAAATATCTCGAATTG	9	173	1
     GGAGATTTAAAAACAAAATTTGCAAAA	4	5	1
CATCAAGTTATTAAGAAATAAAGAATCTGAAC	4	73	1
TGGGCTGAGAATTAGGAAAATATT        	10	121	1
TTAAAATCCAATAAGAACAAAAAAATCACAGA	4	108	1
AGCAACTACCATGGGAAGAAAAATCGTATAGT	6	47	0
CTAGCTGTGCACTAAAAAAATAAGGATCTATT	5	63	1
TATCAAAGCAATAGAAAATAAATCATATAAAA	0	93	1
TAAAGCCTGCTTTTTAAAAATAGTCTGATTCA	7	62	0
AAAAGACTTATCCCTAAAAATAGACTTTTCTA	6	101	1
          **  ********
MAP Score: 10.8879

Motif 7
      ATAACAAAGGGGCTAAAACCAACTATTTAAG	0	4	1
GATTAGCATATCCAAGAGATTTATATCAAAGCAATAG	0	70	1
ATAGCGTCTTCAAAAGAGATTTTTTCCACGTTT    	1	6	0
ATGAAACGTTTGGAAGAGATCATAGACCTTATGAATC	1	41	1
TTGTTTCGTGTGGAAGAGCATCTTAGCATAGGAGTGT	4	153	0
CTGGGTTTTTTTCAAGAGATGCCCTACAATAGATCCT	5	85	0
AATCTGAGTTCGGAGGAGCTTCTTTTAGGAGATTGTA	5	151	0
GACTTTTCTACCGGAGGGATACTGTACCCAATAATAT	6	123	1
AAAGAGGTATCTGGAGAGCTTTCTTACTTTATTCATC	6	163	1
CGAATGAGGTTAAAGGAGATGAATAAAGTAAGAAAGC	6	180	0
CTTCCTCCCCTACAAGGGCTTCACCTCGTGATAAAC 	6	274	1
AATAGTCTGATTCAGGGGCTATGTAACATCATCTTTA	7	39	0
AAAAGCAGGCTTTAGGGGCTTATTTTTCGTAAAAATC	7	80	1
AAGTTTTTTTCTTAAGGGCTGTTTGACAGTCCTTTCC	9	83	1
TTTTTTGAGACAGAGGAGATAATAGGCTCTTTTCTCA	9	226	1
AGGCTCTTTTCTCACGAGCTCCACTCCAAATAGAGTG	9	249	1
CTTCTGTTGTCAAGAGAGATGCGGAGTGGGCATCTCT	10	14	1
          *  ******* *    *
MAP Score: 10.5963

Motif 8
AAAGTAAGACAAGAAGATTAGCATATCCAAGA	0	55	1
ACCACGTCTTTAGAAGCTTCTCTTGCCTTGTA	1	83	1
GCCTTGTATGAAGAGGCTGATCAATTAATGCG	1	107	1
TTTCCGACCAACGGAGCGAATCGTAGCCGGTC	1	186	1
TCGGATATTCTAGAAGATATTCTACTCACTAA	2	57	1
CATCTTAGCATAGGAGTGTTTCTAGATCAATC	4	140	0
CTCCTATGCTAAGATGCTCTTCCACACGAAAC	4	156	1
AATCTCCTAAAAGAAGCTCCTCCGAACTCAGA	5	154	1
AGCAACTAAAAAGGAGCGAGGCTTCCTCCCCT	6	253	1
   GTTTATCACGAGGTGAAGCCCTTGTAGGG	6	281	0
AAGCAGGCTTTAGGGGCTTATTTTTCGTAAAA	7	82	1
AAGAAAAAGCAAGGAGCGAGGTTTTTTCCCAA	7	150	1
 AGCTGACTCACGAGGCGGGACCCTGTTTGGG	7	177	0
TTTTTTTTTCAAGAAGGTGTTCGAAAAAAATA	9	163	1
ATCCTGATGAAAGAGGAGGATC          	9	288	1
          ********  **
MAP Score: 7.77687

Motif 9
TCATTTCGGATATTCTAGAAGATATTCTACTCACTAA	2	52	1
TCACAGAGATTGATCTAGAAACACTCCTATGCTAAGA	4	133	1
TTTCAAGAGATGCCCTACAATAGATCCTTATTTTTTT	5	76	0
CTCTATACAATCTCCTAAAAGAAGCTCCTCCGAACTC	5	146	1
CGAGGCTTCCTCCCCTACAAGGGCTTCACCTCGTGAT	6	269	1
CTCTGGATTTTTACGAAAAATAAGCCCCTAAAGCCTG	7	85	0
GCGAGGTTTTTTCCCAAACAGGGTCCCGCCTCGTGAG	7	165	1
TATTTGTTTGTGTTGTAGAAAAATTCCATTTTTTTTA	9	31	1
CTTTCTTTTTTTTTCAAGAAGGTGTTCGAAAAAAATA	9	158	1
CAATTCGTTGTATTCTACAGACCGTCCCCAGAATACA	10	86	0
          *  **** **    ***
MAP Score: 2.33744

Motif 10
ACGTGGAAAAAATCTCTTTTGAAGACGCTATGAAACGTTTGGAA	1	12	1
TGAATCAACCAACCACGTCTTTAGAAGCTTCTCTTGCCTTGTAT	1	72	1
GTTGGTCGGAAAGCTGTTTAATACGTGCTTCGACTTCTTGAATG	1	154	0
ATCTAGAAACACTCCTATGCTAAGATGCTCTTCCACACGAAACA	4	145	1
TTTTCAAGAGATGCCCTACAATAGATCCTTATTTTTTTAGTGCA	5	70	0
TAAAATGAGAATCTGAGTTCGGAGGAGCTTCTTTTAGGAGATTG	5	153	0
AAAGGAATTAAAGCAACTAAAAAGGAGCGAGGCTTCCTCCCCTA	6	242	1
CTTTTTAAAAATAGTCTGATTCAGGGGCTATGTAACATCATCTT	7	41	0
CTATTTTTAAAAAGCAGGCTTTAGGGGCTTATTTTTCGTAAAAA	7	71	1
ATTAAGAATTAAAGAAAAAGCAAGGAGCGAGGTTTTTTCCCAAA	7	139	1
TTTTTGAGACAGAGGAGATAATAGGCTCTTTTCTCACGAGCTCC	9	227	1
          *  *        *** ***  * *
MAP Score: 0.237364