AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons028_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238407
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	groEL_1	41	Heat Shock Protein-60
#1	groES	117	10 KDa Chaperonin
#2	pepF	97	Oligopeptidase
#3	ybgI	300	ACR family
#4	CPn0776	214	CT605 hypothetical protein
#5	groEL_2	110	heat shock protein-60
#6	groEL_3	300	Heat shock protein-60

Motif 1
TCTAGTTTATTTTTGTTCTGAAGAACTTTTATGATTGCCTG	4	153	1
TTTCTTAATCTTTTGAAATTATAAAGTTTTAACAAGATAGA	4	15	1
TAAGATGACCTTTTCATGGCAGAAGCCTTTCCTGCATTAAG	5	59	1
ACCAAGTCGTTTTTTAGTTCACAATACCTTCAGTAGGAAAG	6	236	0
GAATCCTTAGTTTAAGCGAAAGAAGATTTTATGGTAAGCGA	6	112	0
          TCTTTAAACCAAGATTTGTTCTTGGCTTTTT	2	0	1
GAAAAGGTCATCTTAGAAACAAGAAATATTCCTGTCAAACC	5	33	0
CTCCTTATGTTTTACGTTCTAAGAGACTTTGCTATTTCTGC	1	79	0
GGAACTCCTTTTTAAGAGTCAGGATGAATGAGAAAGCTCAT	2	59	0
ATTGTAAAGGTTTTGTTATAAAAACAAGTAAGTATTCTTAG	3	223	0
CTAGCTAATATCTTACATATAGAATAGTTTGATGAGCTAAG	3	187	1
       GTTTTTAGCACTTAAAATTATTGAGTGCTAAAAT	1	3	1
ACTGCCGAAGTTTATAGAATATGAAATGTAATCCTCTCTAC	3	19	1
TGTTCTTGGCTTTTTCTTAAAGATTGTCTTATAATGAGCTT	2	26	1
CTTTTAGAATTTTACATGGCTTGATGTTTTCCTTTAGAAAT	3	103	0
          ****      * **    ***
MAP Score: 6.71219

Motif 2
TTGCAGAAATAGCAAAGTCTCTTAGAACGTAAA	1	77	1
TTGTTTTTATAACAAAACCTTTACAATAATGGG	3	237	1
    GAATCTTTCTTAATCTTTTGAAATTATAA	4	6	1
ACATTGTATCTACGCAATCGCTAGTAAGGTAGA	4	117	1
TTAGGTTGATTACATAACCTCTTTTTTAAGAGA	6	11	1
GACTAGGGAAATCTTAGTCGTTTTTGAGAGATG	6	59	0
GACTAAGATTTCCCTAGTCTCTAGAATTATGCG	6	73	1
GGCCGAGGCCTGCAAAGCCTCTATCCCCGGTTC	6	188	1
ATTTTTACACTACCAAGTCGTTTTTTAGTTCAC	6	255	0
          * *  ********
MAP Score: 5.96069

Motif 3
ATCACGATAACAAAGCGTTTTTTTTTGTGCAATAATTT	1	40	0
AAAAAGCCAAGAACAAATCTTGGTTTAAAGA       	2	3	0
GATGAGCTAAGAATACTTACTTGTTTTTATAACAAAAC	3	217	1
GGGCACTTGTGTACTAATGCTATTTTTTAAATAAGTCT	3	267	1
CGCTAGTAAGGTAGACATTCTAGTTTATTTTTGTTCTG	4	135	1
ACATCAACAGGCAATCATAAAAGTTCTTCAGAACAAAA	4	163	0
CGGTTTGACAGGAATATTTCTTGTTTCTAAGATGACCT	5	32	1
AGAGACTAGGGAAATCTTAGTCGTTTTTGAGAGATGCA	6	57	0
CAAACCCCCAGTAGACGTAAAATTTTTACACTACCAAG	6	271	0
          * *  * *  * **** *
MAP Score: 5.94511

Motif 4
         GTTTTTAGCACTTAAAATTATT	1	1	1
CACTTAAAATTATTGAGTGCTAAAATTATTG	1	18	1
AAGCGTTTTTTTTTGTGCAATAATTTTAGCA	1	35	0
ACCTTTACAATAATGGGCACTTGTGTACTAA	3	253	1
TCAGCAAGCGTAATGCGCAATTATTAGCCGA	4	57	1
AACCTCTTTTTTAAGAGAACTAAAATGCAAT	6	26	1
TCTTAGTCGTTTTTGAGAGATGCAATTGCAT	6	50	0
GTCTCTAGAATTATGCGCACTTCTCGCTTAC	6	89	1
CTACTGAAGGTATTGTGAACTAAAAAACGAC	6	241	1
          ***** *****
MAP Score: 5.55216

Motif 5
ATCACGATAACAAAGCGTTTTTTTTTGTGC	1	48	0
GCAGAAATAGCAAAGTCTCTTAGAACGTAA	1	79	1
CTCATTATAAGACAATCTTTAAGAAAAAGC	2	34	0
TAAAAGTACAGAAAGACTCTAAATGCATTT	3	138	1
GTTTTTATAACAAAACCTTTACAATAATGG	3	239	1
ATTAGCCGATGAAAATCTTTGTAGTTAAAG	4	79	1
TTTTTGTTCTGAAGAACTTTTATGATTGCC	4	162	1
TTGTTTCTAAGATGACCTTTTCATGGCAGA	5	52	1
AGGTTGATTACATAACCTCTTTTTTAAGAG	6	13	1
CCGAGGCCTGCAAAGCCTCTATCCCCGGTT	6	190	1
          **********
MAP Score: 4.8471

Motif 6
CTTTTTCTTAAAGATTGTCTTATAATGAGCT	2	35	1
ACTCTTAAAAAGGAGTTCCTTCCCTC     	2	81	1
TGTGGTAGAGAGGATTACATTTCATATTCTA	3	33	0
ACATGGCTTGATGTTTTCCTTTAGAAATCTT	3	100	0
TTTAACTACAAAGATTTTCATCGGCTAATAA	4	77	0
AAGAACTTTTATGATTGCCTGTTGATGTTTT	4	173	1
TCTTGTTTCTAAGATGACCTTTTCATGGCAG	5	50	1
AAAAACGACTAAGATTTCCCTAGTCTCTAGA	6	67	1
TAAGCGAAAGAAGATTTTATGGTAAGCGAGA	6	110	0
GCTTAAACTAAGGATTCTCATCCTCCCCTTT	6	136	1
          ****** ****
MAP Score: 3.83627

Motif 7
CAATCACGATAACAAAGCGTTTTTTTTTGTGCAA	1	46	0
AAAAGCCAAGAACAAATCTTGGTTTAAAGA    	2	6	0
    GAGGGAAGGAACTCCTTTTTAAGAGTCAGG	2	77	0
GCACTTGTGTACTAATGCTATTTTTTAAATAAGT	3	269	1
CTAGTAAGGTAGACATTCTAGTTTATTTTTGTTC	4	137	1
GTTTGACAGGAATATTTCTTGTTTCTAAGATGAC	5	34	1
GGTTGATTACATAACCTCTTTTTTAAGAGAACTA	6	14	1
CTCGCTTACCATAAAATCTTCTTTCGCTTAAACT	6	111	1
TTTTTACACTACCAAGTCGTTTTTTAGTTCACAA	6	253	0
          *  ** **** ***
MAP Score: 3.36318

Motif 8
GAACGTAAAACATAAGGAGCATATAA        	1	101	1
CATCCTGACTCTTAAAAAGGAGTTCCTTCCCTC 	2	74	1
TACAGAAAGACTCTAAATGCATTTATAATTACTA	3	144	1
AAACCTTTACAATAATGGGCACTTGTGTACTAAT	3	251	1
AGTCAGCAAGCGTAATGCGCAATTATTAGCCGAT	4	55	1
TTGAAAAAACATCAACAGGCAATCATAAAAGTTC	4	175	0
TTTTAAGAGAACTAAAATGCAATTGCATCTCTCA	6	34	1
TAGTCTCTAGAATTATGCGCACTTCTCGCTTACC	6	87	1
          * *** * *** **
MAP Score: 2.00621