AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons015_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237922
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hisS	300	Histidyl tRNA Synthetase
#1	uhpC	243	Hexosphosphate Transport
#2	minD	32	chromosome partitioning ATPase
#3	thrS	199	Threonyl tRNA Synthetase
#4	alaS	232	Alanyl tRNA Synthetase
#5	CPn0925	159	CT779 hypothetical protein
#6	lysS	300	Lysyl tRNA Synthetase

Motif 1
GTATTTCTTATTTAATTAAAAATAACCAAGAAAA	1	84	1
ATAAAAGTTTTTTTATAAAAAAAAGCTTCTTGCT	3	110	1
AGCTTCTTGCTTTGATCAAAAAAAACACTAAAAT	3	133	1
GCGAAATGCCCTTCATTAAAAAGAGGGTAGATTC	0	184	1
TACCTTGTAATTCTTTCAAAAACAAATGAATTTT	4	83	1
CGCATTTCATCTCAGTGAAAAAGATTTTACACAT	1	207	1
ATCCCTAATTTTTAGTTAAAAAACTTTCCTGTTT	4	135	0
     GTCACTATCCTTAAAAAAACGTGTCGAAT	5	5	1
AATAGCCAATGTTTCTAAAAAAGAGAGGTACGTT	5	134	0
TGTAAACATGCTTCTTAATAAAGAATTTTAAGAA	0	30	1
CTTTGGAACTTGTATTAAAAAATAAAAGTTTTTT	3	89	1
TTCTCCAATACTTAGTTACAAAAACCATAAGCTA	0	93	1
TCTTGATGCGTATCCTCAAAAATCCTTAGCAA  	2	8	0
TCGATCAAATCTCAATAATAAACAGGAAAGTTTT	4	116	1
  GTGATGTCTTCGCTCAAAATGATTACTTTTTT	0	278	0
CCTGGAGACCTTCTATGTAAAAGCAGCAACTATA	4	18	1
CCAGATATTCCATTATCTAAAAAAGTAATCATTT	0	260	1
          ***  * ***** *
MAP Score: 16.5824

Motif 2
AGTATTGGAGAAAAACCGCGCCCTATGAAT	0	75	0
TGGAGCAGTAAAAATACGCTGTTTTAGTAT	1	58	1
ATAACCAAGAAAAACACTCTACTAATGCAT	1	105	1
TGGAACTAATAAAAACATCTTTTATACTAT	3	42	0
TTTTTTTATAAAAAAACTTTTATTTTTTAA	3	103	0
TTTTTTTATAAAAAAAAGCTTCTTGCTTTG	3	117	1
CTTTGATCAAAAAAAACACTAAAATGCTAA	3	142	1
AGCAAAAAGCAAGGAACTCTTACCTTGTAA	4	63	1
ATTTTTAGTTAAAAAACTTTCCTGTTTATT	4	132	0
AGACGAAAATAAAGAACTCTCCTATAATGG	4	171	1
AAGGAATCTGCAAAACCGCTGCCGTTGAGA	4	202	1
       GAAAAAGAACTCTCAACGGCAGC	4	219	0
ACTATCCTTAAAAAAACGTGTCGAATAAGT	5	13	1
          **********
MAP Score: 10.5446

Motif 3
    AATTATCTTTTGTTTTCGTCTGTAAA	0	6	1
CTCGAATCTACCCTCTTTTTAATGAAGGGC	0	191	0
CGATTCCCTCCTTGTTTTTTCATCCTTGAT	1	156	1
TATAAAAAAACTTTTATTTTTTAATACAAG	3	97	0
AAGCAAGAAGCTTTTTTTTATAAAAAAACT	3	115	0
AAAAAAGCTTCTTGCTTTGATCAAAAAAAA	3	128	1
GTTAGGGGGACTTTCGTTGTTAGCATTTTA	3	161	0
GTAAGAGTTCCTTGCTTTTTGCTTGGGGAT	4	56	0
GCAAGGAACTCTTACCTTGTAATTCTTTCA	4	71	1
AGTTAAAAAACTTTCCTGTTTATTATTGAG	4	126	0
CCACAGAGAGCTCTCCTTTTATGGGTACCA	5	103	1
CAAAACGTACCTCTCTTTTTTAGAAACATT	5	131	1
GGTAGTACAGCTCTTGTTTTACTTCTATAA	6	38	0
TCCATGATATCTTTCTTTATGAATCTAAAG	6	104	1
GTGGGATCGGCCTGCTTTTTACAACTTTAG	6	216	1
          **********
MAP Score: 10.0729

Motif 4
TAAGTATTGGAGAAAAACCGCGCCCTATGAATGCTA	0	71	0
AATTTCCCCGAGCAAAACCAAGGCCTATATTCTAAA	6	69	0
ATACTTAGTTACAAAAACCATAAGCTAGCATATAAT	0	100	1
AAAATAACCAAGAAAAACACTCTACTAATGCATCTT	1	102	1
GCAAGGAATCTGCAAAACCGCTGCCGTTGAGAGTTC	4	200	1
AGTCTTGGGTTGGAAAAGCGATATCTATACAAACAT	6	261	1
AGACCTTCTATGTAAAAGCAGCAACTATAGGAAATC	4	23	1
TTTTATGGGTACCAAAACGTACCTCTCTTTTTTAGA	5	119	1
AGGGATAGAGACGAAAATAAAGAACTCTCCTATAAT	4	163	1
AATTTCCATGTGTAAAATCTTTTTCACTGAGATGAA	1	212	0
ATGCGTATCCTCAAAAATCCTTAGCAA         	2	1	0
AATAAGAAATACTAAAACAGCGTATTTTTACTGCTC	1	60	0
CAGCAACTATAGGAAATCCCCAAGCAAAAAGCAAGG	4	41	1
TGTAATTCTTTCAAAAACAAATGAATTTTCGATCAA	4	88	1
AACCCAAGACTCTAAAATCTATCTATCTAAAGTTGT	6	236	0
CATTTATAGAAGTAAAACAAGAGCTGTACTACCATT	6	35	1
ATGTTTACAGACGAAAACAAAAGATAATT       	0	3	0
          ** ******     **
MAP Score: 9.80051

Motif 5
TCGTGCGCGTAGCGCGCTCCTGGATTATCTC	0	141	1
AACCAAGAAAAACACTCTACTAATGCATCTT	1	107	1
AAAAGCAAGGAACTCTTACCTTGTAATTCTT	4	67	1
TTTTAGTTAAAAAACTTTCCTGTTTATTATT	4	129	0
ACGAAAATAAAGAACTCTCCTATAATGGCAA	4	173	1
TTATCCACAGAGAGCTCTCCTTTTATGGGTA	5	99	1
TATGGGTACCAAAACGTACCTCTCTTTTTTA	5	122	1
AAGTAAAACAAGAGCTGTACTACCATTTAGA	6	44	1
TTATGAATCTAAAGTTTTCCTAGAGCGAAGA	6	120	1
          ****** ****
MAP Score: 5.08749

Motif 6
GTCTGTAAACATGCTTCTTAATAAAGAATTTTAA	0	27	1
AATATGACTTAGGCTTAGGCAGGAGTCACTAAGC	0	225	1
CAGTAAAAATACGCTGTTTTAGTATTTCTTATTT	1	63	1
    TTGCTAAGGATTTTTGAGGATACGCATCAA	2	6	1
CCAGTTTGTAATGTTTATTAAGCAGATAGTATAA	3	17	1
TAAAAAATAAAAGTTTTTTTATAAAAAAAAGCTT	3	104	1
ATAAACAGGAAAGTTTTTTAACTAAAAATTAGGG	4	133	1
CGTGTCGAATAAGTTTGTTGAGTATGATGACACT	5	29	1
ATTCCATGATATCTTTCTTTATGAATCTAAAGTT	6	102	1
          * **** ** ** *
MAP Score: 2.76007