AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239556
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0034_TP0035	197	TP0034: ABC transporter, periplasmic binding protein, TP0035: ABC transporter, ATP-binding protein
#1	TP0163	174	ABC transporter, periplasmic binding protein (troA)
#2	TP0164	147	ABC transporter, ATP-binding protein (troB)

Motif 1
GAGAGTGTGCGAGTACGCGCCCGTTTGGGGTGGAAGCCC	0	152	1
CCCGTTTGGGGTGGAAGCCCCTTCAAAGGAGCCATC   	0	171	1
        AAGAGGGCGCAACTGTAGCTGCTTATGCGAG	1	2	1
GTAGCTCGAGAGGTCCGCGCCAGAGTGCCGTTTTCTTTT	1	65	1
AGTTGAGTGGGTAGAAGAGCCGTTGGTGGTCGGCTGTAC	2	22	1
GGTCGGCTGTACGGCAGCGCCTGTTCACGACGTGGTGAT	2	49	1
ATTAGTGAAGGAGGTGGCGCGCTCACCGCTGACGGCTCT	2	86	1
TCGCTCAATCGGGTAAGAGCCGTCAGCGGTGAGCGCGCC	2	101	0
          * **  ***** *     *
MAP Score: 9.04056

Motif 2
CTATTTTTATGAATGCAACACTACTGTCTCTGAGAAAAAA	0	19	1
CACCCCAAACGGGCGCGTACTCGCACACTCTCTGCAAAAT	0	144	0
CGTTTGGGGTGGAAGCCCCTTCAAAGGAGCCATC      	0	173	1
        AAGAGGGCGCAACTGTAGCTGCTTATGCGAGG	1	2	1
CGGACCTCTCGAGCTACATGATAAAGAAGCATTTGATCTT	1	42	0
TGTAGCTCGAGAGGTCCGCGCCAGAGTGCCGTTTTCTTTT	1	64	1
CGTTTCCTGCGTGATCCGCTACTTTGATGCATCAAAATTC	1	128	1
AGAGCCGTTGGTGGTCGGCTGTACGGCAGCGCCTGTTCAC	2	37	1
AGGAGGTGGCGCGCTCACCGCTGACGGCTCTTACCCGATT	2	94	1
          * * *** *  *   *  **
MAP Score: 6.76058

Motif 3
GTAGCTCGAGAGGTCCGCGCCAGAGTGCCGTTT	1	65	1
GAGAGTGTGCGAGTACGCGCCCGTTTGGGGTGG	0	152	1
GCCGTCAGCGGTGAGCGCGCCACCTCCTTCACT	2	89	0
GGTCGGCTGTACGGCAGCGCCTGTTCACGACGT	2	49	1
        AAGAGGGCGCAACTGTAGCTGCTTA	1	2	1
TGAGAAAAAAGAGACCACAGCTGCACAATGCAA	0	49	1
CTTTCAGGAAAAGAAAACGGCACTCTGGCGCGG	1	79	0
          * * ******* *
MAP Score: 6.50646

Motif 4
GAGAGTGTGCGAGTACGCGCCCGTTTGGGGTGGAAGCCCCTT	0	152	1
CCCGTTTGGGGTGGAAGCCCCTTCAAAGGAGCCATC      	0	171	1
CATGTAGCTCGAGAGGTCCGCGCCAGAGTGCCGTTTTCTTTT	1	62	1
GACGTTTCCTGCGTGATCCGCTACTTTGATGCATCAAAATTC	1	126	1
GAAGAGCCGTTGGTGGTCGGCTGTACGGCAGCGCCTGTTCAC	2	35	1
GAAGGAGGTGGCGCGCTCACCGCTGACGGCTCTTACCCGATT	2	92	1
          * * * ** **  *   *   *
MAP Score: 5.56548

Motif 5
TTTTTTCTCAGAGACAGTAGTGTTGCATTCATAAAAATA	0	20	0
CCTCGCATAAGCAGCTACAGTTGCGCCCTCTT       	1	3	0
TCTTTATCATGTAGCTCGAGAGGTCCGCGCCAGAGTGCC	1	55	1
AAAAATTGACGTTTCCTGCGTGATCCGCTACTTTGATGC	1	119	1
GTGGGTAGAAGAGCCGTTGGTGGTCGGCTGTACGGCAGC	2	28	1
CGGCTGTACGGCAGCGCCTGTTCACGACGTGGTGATTAG	2	52	1
GTGGTGATTAGTGAAGGAGGTGGCGCGCTCACCGCTGAC	2	80	1
          *   *    ***  *****
MAP Score: 2.98934

Motif 6
CTGTCTCTGAGAAAAAAGAGACCACAGCTGCACAATGCAAATTGT	0	42	1
GTACGCGCCCGTTTGGGGTGGAAGCCCCTTCAAAGGAGCCATC  	0	164	1
TCTTTATCATGTAGCTCGAGAGGTCCGCGCCAGAGTGCCGTTTTC	1	55	1
AAAAATTGACGTTTCCTGCGTGATCCGCTACTTTGATGCATCAAA	1	119	1
TAGAAGAGCCGTTGGTGGTCGGCTGTACGGCAGCGCCTGTTCACG	2	33	1
AGCCGTCAGCGGTGAGCGCGCCACCTCCTTCACTAATCACCACGT	2	78	0
          *      * *    * *** **  *
MAP Score: 2.60502

Motif 7
CTCTACCATGGTTTTCGAAGAAATTCCCGTTCAACATCCT	0	89	1
TTTGCAGAGAGTGTGCGAGTACGCGCCCGTTTGGGGTGGA	0	146	1
        AAGAGGGCGCAACTGTAGCTGCTTATGCGAGG	1	2	1
CTTTATCATGTAGCTCGAGAGGTCCGCGCCAGAGTGCCGT	1	56	1
AGAGCCGTTGGTGGTCGGCTGTACGGCAGCGCCTGTTCAC	2	37	1
GCCGTCAGCGGTGAGCGCGCCACCTCCTTCACTAATCACC	2	82	0
          *** ***      * **  *
MAP Score: 1.18957

Motif 8
GCTTCTTTATCATGTAGCTCGAGAGGTCCGCGCCAGAGTGC	1	52	1
CTGAAAAATTGACGTTTCCTGCGTGATCCGCTACTTTGATG	1	116	1
TGAGTGGGTAGAAGAGCCGTTGGTGGTCGGCTGTACGGCAG	2	25	1
GGTGATTAGTGAAGGAGGTGGCGCGCTCACCGCTGACGGCT	2	82	1
          ** *   *    * * ** **
MAP Score: 0.991357

Motif 9
CTCTACCATGGTTTTCGAAGAAATTCCCGTTCAACATCCT	0	89	1
ATATTTTGCAGAGAGTGTGCGAGTACGCGCCCGTTTGGGG	0	142	1
GTACGCGCCCGTTTGGGGTGGAAGCCCCTTCAAAGGAGCC	0	164	1
CCTCGCATAAGCAGCTACAGTTGCGCCCTCTT        	1	2	0
TGATAAAGAAGCATTTGATCTTCCTCGCATAAGCAGCTAC	1	24	0
TCTTTATCATGTAGCTCGAGAGGTCCGCGCCAGAGTGCCG	1	55	1
ATGTAGAGTTGAGTGGGTAGAAGAGCCGTTGGTGGTCGGC	2	16	1
GTCGTGAACAGGCGCTGCCGTACAGCCGACCACCAACGGC	2	40	0
GTGGTGATTAGTGAAGGAGGTGGCGCGCTCACCGCTGACG	2	80	1
          *    **  * **  *** *
MAP Score: 0.445288