AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons017_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239570
 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
CTCTATTTTTATGAATGCAACACTACTGTCTCTGAGAAAAAA	0	17	1
GAGAGTGTGCGAGTACGCGCCCGTTTGGGGTGGAAGCCCCTT	0	152	1
CCCGTTTGGGGTGGAAGCCCCTTCAAAGGAGCCATC      	0	171	1
          AAGAGGGCGCAACTGTAGCTGCTTATGCGAGG	1	0	1
CATGTAGCTCGAGAGGTCCGCGCCAGAGTGCCGTTTTCTTTT	1	62	1
GACGTTTCCTGCGTGATCCGCTACTTTGATGCATCAAAATTC	1	126	1
GAAGAGCCGTTGGTGGTCGGCTGTACGGCAGCGCCTGTTCAC	2	35	1
GAAGGAGGTGGCGCGCTCACCGCTGACGGCTCTTACCCGATT	2	92	1
          * * * ** **  *   *   *
MAP Score: 8.82901

Motif 2
          AAGAGGGCGCAACTGTAGCT	1	0	1
CTTCCACCCCAAACGGGCGCGTACTCGCAC	0	158	0
TTCTTTTCCTGAAAGGGTACTGAAAAATTG	1	97	1
AATCGGGTAAGAGCCGTCAGCGGTGAGCGC	2	104	0
GTGGGTAGAAGAGCCGTTGGTGGTCGGCTG	2	28	1
ACCACGTCGTGAACAGGCGCTGCCGTACAG	2	55	0
ATTAGTGAAGGAGGTGGCGCGCTCACCGCT	2	86	1
ATATTTTGCAGAGAGTGTGCGAGTACGCGC	0	142	1
ATGTAGAGTTGAGTGGGTAGAAGAGCCGTT	2	16	1
CATGTAGCTCGAGAGGTCCGCGCCAGAGTG	1	62	1
TCAGGAAAAGAAAACGGCACTCTGGCGCGG	1	79	0
TTTTTTCTCAGAGACAGTAGTGTTGCATTC	0	29	0
GAGCGAAAAGAAGGGAGCAGTAT       	2	134	1
          **********
MAP Score: 8.38656

Motif 3
TTTTTTCTCAGAGACAGTAGTGTTGCATTCATAAA	0	24	0
TACTGTCTCTGAGAAAAAAGAGACCACAGCTGCAC	0	40	1
ATGGTTTTCGAAGAAATTCCCGTTCAACATCCTAA	0	96	1
GGCTCCTTTGAAGGGGCTTCCACCCCAAACGGGCG	0	169	0
TTCCTCGCATAAGCAGCTACAGTTGCGCCCTCTT 	1	9	0
CTGCTTATGCGAGGAAGATCAAATGCTTCTTTATC	1	28	1
CATGTAGCTCGAGAGGTCCGCGCCAGAGTGCCGTT	1	62	1
CTTTCAGGAAAAGAAAACGGCACTCTGGCGCGGAC	1	77	0
ATGTAGAGTTGAGTGGGTAGAAGAGCCGTTGGTGG	2	16	1
ACGTCGTGAACAGGCGCTGCCGTACAGCCGACCAC	2	47	0
GTGATTAGTGAAGGAGGTGGCGCGCTCACCGCTGA	2	83	1
AATCGGGTAAGAGCCGTCAGCGGTGAGCGCGCCAC	2	99	0
TTACCCGATTGAGCGAAAAGAAGGGAGCAGTAT  	2	124	1
          *** ** * ***  *
MAP Score: 2.38021

Motif 4
CTCTCTACCATGGTTTTCGAAGAAATTCCCGTTCAACATCCTAAAAA	0	87	1
TAAAAAGGAATTGCATATTTTGCAGAGAGTGTGCGAGTACGCGCCCG	0	128	1
CATTTGATCTTCCTCGCATAAGCAGCTACAGTTGCGCCCTCTT    	1	6	0
GATCAAATGCTTCTTTATCATGTAGCTCGAGAGGTCCGCGCCAGAGT	1	44	1
        CGTGGAATGTAGAGTTGAGTGGGTAGAAGAGCCGTTGGT	2	2	1
CCGTTGGTGGTCGGCTGTACGGCAGCGCCTGTTCACGACGTGGTGAT	2	41	1
GTTCACGACGTGGTGATTAGTGAAGGAGGTGGCGCGCTCACCGCTGA	2	71	1
          * *    *   * **   * *  *  *
MAP Score: 1.12433