AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons025_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239804
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0099	194	uridylate kinase (smbA)
#1	TP0185	147	signal peptidase I (sip)
#2	TP0186	54	oxygen-independent coproporphyrinogen III oxidase, putative
#3	TP0215	205	grpE protein (grpE)
#4	TP0216	115	heat shock protein 70 (dnaK)
#5	TP0843	92	heat shock protein, putative

Motif 1
GGTGCGTGCTGCGCATCGTGCTGTTCCTTTTAT	2	30	1
CGGCTATACTGCGCGCCCTGCAGGCAGGGCGGG	4	66	1
GAACACTCCATCGCCCCGTGCACGCTGGGACGC	0	102	1
ATAGCGTTGCGCGGGATGTGTGCTCTTTTTAGA	5	23	0
        TTGCCCAACCTCCTCTAAAAAGAGC	5	2	1
GGGATGCAGGTCGCATCGTGGTCGGTGTAGTCA	3	88	1
        TCGCGCATCCTCGTGATATGAGGTT	3	2	1
 TGTGTAGGCGCCGCATTTGTGGTGCGTGCTGC	2	9	1
GGGTTCCTGTGCCCCTCATGGCGCCGGATGCTA	1	51	1
TTGACCGAGGGCGGCGTCTCTCGTTACTTTTAC	3	141	1
GGCACGTCAATCCCTCTTTGCTGTAGGGCTCCC	5	69	1
TAGGTGGTTGTCCGTTTCTGTGCTTGGCAGTTA	3	50	1
TTGGATCCAGGCCCTGTGTGTATCTGGCATTGC	0	133	0
AGTTTTTACGTCGGTTTTTGCACAGAATACAAG	0	43	1
AGGAGTCTGTGTCGCCCGTGTAGAACACTCCAT	0	80	1
GTGTTAGGCTGCCGTGTCTGGGAGGGACGCCGT	1	121	1
          ****  ***** *
MAP Score: 16.7965

Motif 2
CTGGCATTGCGTCCCAGCGTGCACGGGGCGATGGAGTGTTCTA	0	100	0
TTTGGATCCAGGCCCTGTGTGTATCTGGCATTGCGTCCCAGCG	0	124	0
GATCCAAAGGGTCTCTTTGCGTTACGATGCCGGCGAGAGGGTT	0	159	1
TGCCCCTCATGGCGCCGGATGCTACCGGATAGGCACTTCCCTT	1	60	1
TTCGATTATCGCCGTGTTAGGCTGCCGTGTCTGGGAGGGACGC	1	108	1
GCGCCGCATTTGTGGTGCGTGCTGCGCATCGTGCTGTTCCTTT	2	17	1
GCGCATCCTCGTGATATGAGGTTCCGTCCCAAGGACGTTAGGT	3	12	1
AGGACGTTAGGTGGTTGTCCGTTTCTGTGCTTGGCAGTTACCA	3	43	1
TTACCATTGGGATGCAGGTCGCATCGTGGTCGGTGTAGTCAGA	3	80	1
GACCGAGGGCGGCGTCTCTCGTTACTTTTACGGCATTACCGCG	3	143	1
        CAGGCAGGGTATGCTGAGAGGTCAGGATGGAGTTC	4	2	1
GGTCAGGATGGAGTTCTGGAGCACCGGTGCTAGGTAACGGCTA	4	29	1
GCGCCCTGCAGGCAGGGCGGGTATCCTATACAGAGGAGTTGAG	4	78	1
CCGATCTTTTTTCAGATAGCGTTGCGCGGGATGTGTGCTCTTT	5	28	0
          * * * *   *** **      *
MAP Score: 16.1351

Motif 3
CGTGCACGGGGCGATGGAGTGTTCTACACGGGCGACACAGA	0	85	0
ATTGAAAAAAGCCTTGCGGTTCTTTGCAATGAGATGGGTTC	1	16	1
GCAATGAGATGGGTTCCTGTGCCCCTCATGGCGCCGGATGC	1	41	1
GGAACAGCACGATGCGCAGCACGCACCACAAATGCGGCGCC	2	16	0
GCATCCTCGTGATATGAGGTTCCGTCCCAAGGACGTTAGGT	3	14	1
ACGTTAGGTGGTTGTCCGTTTCTGTGCTTGGCAGTTACCAT	3	46	1
AGTTACCATTGGGATGCAGGTCGCATCGTGGTCGGTGTAGT	3	78	1
AAAGTAACGAGAGACGCCGCCCTCGGTCAAGAAAACACCTA	3	130	0
CCTAGCACCGGTGCTCCAGAACTCCATCCTGACCTCTCAGC	4	22	0
CTAGGTAACGGCTATACTGCGCGCCCTGCAGGCAGGGCGGG	4	58	1
AAGAGGGATTGACGTGCCGATCTTTTTTCAGATAGCGTTGC	5	46	0
          * * *** *  * *  *   *
MAP Score: 12.3454

Motif 4
AGTTACCATTGGGATGCAGGTCGCATCGTG	3	78	1
AGATAGCGTTGCGCGGGATGTGTGCTCTTT	5	28	0
TGCCGTGTCTGGGAGGGACGCCGTTTT   	1	130	1
CGTGCACGGGGCGATGGAGTGTTCTACACG	0	96	0
TCTTTGCGTTACGATGCCGGCGAGAGGGTT	0	172	1
GCCCCTCATGGCGCCGGATGCTACCGGATA	1	61	1
GCGCCCTGCAGGCAGGGCGGGTATCCTATA	4	78	1
GTTTTCTTGACCGAGGGCGGCGTCTCTCGT	3	135	1
CTGAGAGGTCAGGATGGAGTTCTGGAGCAC	4	23	1
TCGCCGTGTTAGGCTGCCGTGTCTGGGAGG	1	116	1
   TGTGTAGGCGCCGCATTTGTGGTGCGT	2	7	1
CGGCATTACCGCGAGGGTGTTATGGCAAAA	3	173	1
CGGCTATACTGCGCGCCCTGCAGGCAGGGC	4	66	1
TCATATCACGAGGATGCGCGA         	3	1	0
ACAGCAAAGAGGGATTGACGTGCCGATCTT	5	63	0
CGTGCACGCTGGGACGCAATGCCAGATACA	0	118	1
CTCTCAGCATACCCTGCCTG          	4	0	0
ACAGCACGATGCGCAGCACGCACCACAAAT	2	24	0
          **********
MAP Score: 10.2414

Motif 5
AATACAAGAACTAGGAGTCTGTGTCGCCCGTGT	0	68	1
TCCCAGCGTGCACGGGGCGATGGAGTGTTCTAC	0	99	0
CCCGTGCACGCTGGGACGCAATGCCAGATACAC	0	116	1
CCTTTGGATCCAGGCCCTGTGTGTATCTGGCAT	0	136	0
TTGCAAAGAACCGCAAGGCTTTTTTCAATTACC	1	12	0
GCTGCCGTGTCTGGGAGGGACGCCGTTTT    	1	128	1
GGTTCCGTCCCAAGGACGTTAGGTGGTTGTCCG	3	31	1
GCAGTTACCATTGGGATGCAGGTCGCATCGTGG	3	76	1
GTTTTCTTGACCGAGGGCGGCGTCTCTCGTTAC	3	135	1
TACGGCATTACCGCGAGGGTGTTATGGCAAAAA	3	171	1
          CAGGCAGGGTATGCTGAGAGGTC	4	0	1
GCAGGGTATGCTGAGAGGTCAGGATGGAGTTCT	4	13	1
GCCCTGCCTGCAGGGCGCGCAGTATAGCCGTTA	4	63	0
GCGCGCCCTGCAGGCAGGGCGGGTATCCTATAC	4	76	1
TCAGATAGCGTTGCGCGGGATGTGTGCTCTTTT	5	27	0
AGCCCTACAGCAAAGAGGGATTGACGTGCCGAT	5	66	0
          * *******  **
MAP Score: 4.74577

Motif 6
AATACAAGAACTAGGAGTCTGTGTCGCCCGTGT	0	68	1
CCCGTGCACGCTGGGACGCAATGCCAGATACAC	0	116	1
CAGATACACACAGGGCCTGGATCCAAAGGGTCT	0	140	1
GTTACGATGCCGGCGAGAGGGTTTC        	0	179	1
GTGCCCCTCATGGCGCCGGATGCTACCGGATAG	1	59	1
GCTGCCGTGTCTGGGAGGGACGCCGTTTT    	1	128	1
     TGTGTAGGCGCCGCATTTGTGGTGCGTG	2	5	1
GTGGTGCGTGCTGCGCATCGTGCTGTTCCTTTT	2	28	1
ACACCGACCACGATGCGACCTGCATCCCAATGG	3	83	0
TTTTCTTGACCGAGGGCGGCGTCTCTCGTTACT	3	136	1
GGATGGAGTTCTGGAGCACCGGTGCTAGGTAAC	4	34	1
AACGGCTATACTGCGCGCCCTGCAGGCAGGGCG	4	64	1
GCCCTGCAGGCAGGGCGGGTATCCTATACAGAG	4	80	1
TCAGATAGCGTTGCGCGGGATGTGTGCTCTTTT	5	27	0
GAAAAAAGATCGGCACGTCAATCCCTCTTTGCT	5	58	1
          ******* *  **
MAP Score: 3.5505

Motif 7
AGTCTGTGTCGCCCGTGTAGAACACTCCATCGCC	0	83	1
ACTCCATCGCCCCGTGCACGCTGGGACGCAATGC	0	106	1
TTGGATCCAGGCCCTGTGTGTATCTGGCATTGCG	0	132	0
AAAAAGCCTTGCGGTTCTTTGCAATGAGATGGGT	1	21	1
GGGTTCCTGTGCCCCTCATGGCGCCGGATGCTAC	1	51	1
GCCCCTCATGGCGCCGGATGCTACCGGATAGGCA	1	61	1
TTCGATTATCGCCGTGTTAGGCTGCCGTGTCTGG	1	108	1
GTGTTAGGCTGCCGTGTCTGGGAGGGACGCCGTT	1	121	1
   TGTGTAGGCGCCGCATTTGTGGTGCGTGCTG	2	7	1
ACAGCACGATGCGCAGCACGCACCACAAATGCGG	2	20	0
CCAAGGACGTTAGGTGGTTGTCCGTTTCTGTGCT	3	40	1
TCGCATCGTGGTCGGTGTAGTCAGACGGTAAATA	3	98	1
AACGAGAGACGCCGCCCTCGGTCAAGAAAACACC	3	132	0
CGGCTATACTGCGCGCCCTGCAGGCAGGGCGGGT	4	66	1
TAGGATACCCGCCCTGCCTGCAGGGCGCGCAGTA	4	72	0
GCTCTTTTTAGAGGAGGTTGGGCAA         	5	1	0
AGATAGCGTTGCGCGGGATGTGTGCTCTTTTTAG	5	24	0
          **** ** ***  *
MAP Score: 3.24162

Motif 8
GTCGGTGTAGTCAGACGGTAAATAGGTGTTTTCTTG	3	108	1
     GGGAGCCCTACAGCAAAGAGGGATTGACGTG	5	71	0
ACCGCGAGGGTGTTATGGCAAAAAAGGAGAAGAAA 	3	180	1
CAGGAACCCATCTCATTGCAAAGAACCGCAAGGCTT	1	24	0
         ATGGTAATTGAAAAAAGCCTTGCGGTT	1	1	1
CTCGCCGGCATCGTAACGCAAAGAGACCCTTTGGAT	0	160	0
TCCCGCGCAACGCTATCTGAAAAAAGATCGGCACGT	5	40	1
GCGGTAATGCCGTAAAAGTAACGAGAGACGCCGCCC	3	149	0
          **  *  * *** ***
MAP Score: 1.3271

Motif 9
CCCAGCGTGCACGGGGCGATGGAGTGTTCT	0	101	0
CGCCCCGTGCACGCTGGGACGCAATGCCAG	0	113	1
TGCCAGATACACACAGGGCCTGGATCCAAA	0	137	1
TGCGTTACGATGCCGGCGAGAGGGTTTC  	0	176	1
ATCCGGTAGCATCCGGCGCCATGAGGGGCA	1	60	0
CGGCAGCCTAACACGGCGATAATCGAATTG	1	105	0
TGCCGTGTCTGGGAGGGACGCCGTTTT   	1	130	1
CGCACCACAAATGCGGCGCCTACACA    	2	6	0
ACAGCACGATGCGCAGCACGCACCACAAAT	2	24	0
  GATAAAAGGAACAGCACGATGCGCAGCA	2	36	0
TCATATCACGAGGATGCGCGA         	3	1	0
AGTTACCATTGGGATGCAGGTCGCATCGTG	3	78	1
TCTTGACCGAGGGCGGCGTCTCTCGTTACT	3	139	1
GGTAACGGCTATACTGCGCGCCCTGCAGGC	4	61	1
CGCGCCCTGCAGGCAGGGCGGGTATCCTAT	4	77	1
AGATAGCGTTGCGCGGGATGTGTGCTCTTT	5	28	0
          **********
MAP Score: 0.289237