AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons012_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239297
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0075	118	sugar ABC transporter, permease protein (y4oQ)
#1	TP0076	39	sugar ABC transporter, permease protein (y4oR)
#2	TP0144	109	thiamine ABC transporter, thiamine-binding periplasmic protein, putative
#3	TP0652	175	spermidine/putrescine ABC transporter, ATP-binding protein (potA)
#4	TP0655	35	spermidine/putrescine ABC transporter, periplasmic binding protein (potD)
#5	TP0737	233	sugar ABC transporter, periplasmic binding protein (msmE)

Motif 1
ACGCTACCCAACGTAACGCGCTCCACAGAT	0	84	0
ACGTTGGGTAGCGTAAGAGGGGGAGTGC  	0	100	1
     GGGTTGCGTACGGGTTAGATAAGAG	1	5	1
          GCGGGCGAGTGTACCGAATG	2	0	1
CTCCTATCCAGGGTGAGGGGTACAGTGCTG	2	51	0
TGCTATAGTCCCCGGCGGGGAGAGGCT   	2	92	1
       AATGCGTAAGACGGGGTGGTCCT	3	3	1
CGCGAGAAGTGCGCATGAGGAAGAAAGGAC	3	28	0
ACGCTCGCTGGCGCGAGAAGTGCGCATGAG	3	39	0
GCGCCAGCGAGCGTAACACGCCAGCGGTAA	3	55	1
CGGTTGGGGTACGCAAGGCGTCCGTGTGTC	3	98	0
GTCAAGGCTCGCGGTTGGGGTACGCAAGGC	3	109	0
CATTGCGGAGGCCGATGGTGCGGTATTTGG	3	148	0
GCAAACAATCTCGTAAGGAGCAAAGC    	4	19	1
GAGAAAAGCAGCGGTCGGCGCGTTAGTTGC	5	109	0
TGCACGCAAAACCTGCCAGGAAACAATGAT	5	139	0
CCTTCTCGGCGCCGATGGCGTTTTGCTTGA	5	177	0
GAACAGATATACGTGTCGGGGAGGTTTAC 	5	214	1
          **********
MAP Score: 18.4915

Motif 2
ATGCTATAGTCCCCGGCGGGGAGAGGCT  	2	91	1
GCACTTCTCGCGCCAGCGAGCGTAACACGC	3	46	1
GAGCGTAACACGCCAGCGGTAATCTGTCCA	3	63	1
GCCTTGCGTACCCCAACCGCGAGCCTTGAC	3	109	1
CCAAATACCGCACCATCGGCCTCCGCAATG	3	148	1
GCAACTAACGCGCCGACCGCTGCTTTTCTC	5	109	1
TCAAGCAAAACGCCATCGGCGCCGAGAAGG	5	177	1
          **********
MAP Score: 13.2889

Motif 3
      AAAGTCTCTTCTTCTTGGGGGAAGAGAGGGCAGAAA	0	4	1
GCGTTACGTTGGGTAGCGTAAGAGGGGGAGTGC         	0	95	1
          GGGTTGCGTACGGGTTAGATAAGAGCAGGAGC	1	0	1
CAGTGCTGCTGTCTTGCTCAAAGGGAGTGCATTCGGTACACT	2	17	0
TAGAGCTCCTATCCAGGGTGAGGGGTACAGTGCTGCTGTCTT	2	44	0
         AGCCTCTCCCCGCCGGGGACTATAGCATAGCTC	2	86	0
GCTGGCGCGAGAAGTGCGCATGAGGAAGAAAGGACCACCCCG	3	21	0
GCCAGCGAGCGTAACACGCCAGCGGTAATCTGTCCAGCAAGG	3	57	1
GTTGGGGTACGCAAGGCGTCCGTGTGTCCTTGCTGGACAGAT	3	84	0
GGTATGTTCTGTCAAGGCTCGCGGTTGGGGTACGCAAGGCGT	3	107	0
TCCTTCTCATTGCGGAGGCCGATGGTGCGGTATTTGGGTATG	3	143	0
ACTTTCTGCAAACAATCTCGTAAGGAGCAAAGC         	4	12	1
ATCCCTCCGAGAGTTTGGTCGAAGGAGGCATGGCT       	5	3	0
GAAAAGCAGCGGTCGGCGCGTTAGTTGCCTTGTGCGACAGAG	5	95	0
AGGACTGCACGCAAAACCTGCCAGGAAACAATGATGAGAAAA	5	132	0
CCTCATTCAAGCAAAACGCCATCGGCGCCGAGAAGGGTCCGA	5	171	1
CCGATGAACAGATATACGTGTCGGGGAGGTTTAC        	5	209	1
          *     ****   ** *   **
MAP Score: 11.9632

Motif 4
         GCACTCCCCCTCTTACGCTACC	0	106	0
GCTCTTATCTAACCCGTACGCAACCC     	1	5	0
GCATTCGGTACACTCGCCCGC          	2	0	0
TATGCTATAGTCCCCGGCGGGGAGAGGCT  	2	90	1
GGAAGAAAGGACCACCCCGTCTTACGCATT 	3	9	0
ATGCGCACTTCTCGCGCCAGCGAGCGTAACA	3	42	1
CAGCGAGCGTAACACGCCAGCGGTAATCTGT	3	59	1
CCAGCAAGGACACACGGACGCCTTGCGTACC	3	90	1
CGCCTTGCGTACCCCAACCGCGAGCCTTGAC	3	108	1
AAATACCGCACCATCGGCCTCCGCAATGAGA	3	150	1
TTCGACCAAACTCTCGGAGGGATGGATGATA	5	22	1
CAAGGCAACTAACGCGCCGACCGCTGCTTTT	5	105	1
AAGCAAAACGCCATCGGCGCCGAGAAGGGTC	5	179	1
          *** *******
MAP Score: 8.40078

Motif 5
  AAAGTCTCTTCTTCTTGGGGGAAGAGAGGGCAGAAAAGATGCTGG	0	8	1
AGAGAGGGCAGAAAAGATGCTGGATATGAGCGGAAACAGAATGACGT	0	32	1
ACGTGTTCTATCTGTGGAGCGCGTTACGTTGGGTAGCGTAAGAGGGG	0	75	1
GTACAGTGCTGCTGTCTTGCTCAAAGGGAGTGCATTCGGTACACTCG	2	15	0
GGCGTGTTACGCTCGCTGGCGCGAGAAGTGCGCATGAGGAAGAAAGG	3	30	0
CACTTCTCGCGCCAGCGAGCGTAACACGCCAGCGGTAATCTGTCCAG	3	47	1
CCAGCGGTAATCTGTCCAGCAAGGACACACGGACGCCTTGCGTACCC	3	75	1
TCTCATCATTGTTTCCTGGCAGGTTTTGCGTGCAGTCCTCATTCAAG	5	135	1
CGTGCAGTCCTCATTCAAGCAAAACGCCATCGGCGCCGAGAAGGGTC	5	163	1
          **   *  **  *    *   **   *
MAP Score: 7.30205

Motif 6
AAGACAGCAGCACTGTACCCCTCACCCTGGATAGGAGCTC	2	44	1
CACACGGACGCCTTGCGTACCCCAACCGCGAGCCTTGACA	3	100	1
CCAAATACCGCACCATCGGCCTCCGCAATGAGAAGGA   	3	148	1
ATCTTTTCTGCCCTCTCTTCCCCCAAGAAGAAGAGACTTT	0	10	0
TCTAGAGCTATGCTATAGTCCCCGGCGGGGAGAGGCT   	2	82	1
ACGCGCCGACCGCTGCTTTTCTCATCATTGTTTCCTGGCA	5	116	1
TCCTCATGCGCACTTCTCGCGCCAGCGAGCGTAACACGCC	3	37	1
TCAAGCAAAACGCCATCGGCGCCGAGAAGGGTCCGATGAA	5	177	1
   GCACTCCCCCTCTTACGCTACCCAACGTAACGCGCTC	0	91	0
          * ** *   ****  *   *
MAP Score: 6.47337

Motif 7
CATCTTTTCTGCCCTCTCTTCCCCCAAGAAGAAGAGAC	0	13	0
  GCACTCCCCCTCTTACGCTACCCAACGTAACGCGCT	0	92	0
CTCAAAGGGAGTGCATTCGGTACACTCGCCCGC     	2	5	0
GGGTACAGTGCTGCTGTCTTGCTCAAAGGGAGTGCATT	2	26	0
GACAGCAGCACTGTACCCCTCACCCTGGATAGGAGCTC	2	46	1
GTCCTTTCTTCCTCATGCGCACTTCTCGCGCCAGCGAG	3	28	1
TGTCCAGCAAGGACACACGGACGCCTTGCGTACCCCAA	3	87	1
GCCTTGCGTACCCCAACCGCGAGCCTTGACAGAACATA	3	109	1
AAATACCGCACCATCGGCCTCCGCAATGAGAAGGA   	3	150	1
AGCCATGCCTCCTTCGACCAAACTCTCGGAGGGATGGA	5	10	1
CAGGTTTTGCGTGCAGTCCTCATTCAAGCAAAACGCCA	5	154	1
          ** *   **  * *** *
MAP Score: 3.52171

Motif 8
CTTCTTGGGGGAAGAGAGGGCAGAAAAGATGCTGGATATGAG	0	20	1
TTCTATCTGTGGAGCGCGTTACGTTGGGTAGCGTAAGAGGGG	0	80	1
       GCGGGCGAGTGTACCGAATGCACTCCCTTTGAGCA	2	3	1
GTTACGCTCGCTGGCGCGAGAAGTGCGCATGAGGAAGAAAGG	3	30	0
ACTTCTCGCGCCAGCGAGCGTAACACGCCAGCGGTAATCTGT	3	48	1
ACACGGACGCCTTGCGTACCCCAACCGCGAGCCTTGACAGAA	3	101	1
TCATTGTTTCCTGGCAGGTTTTGCGTGCAGTCCTCATTCAAG	5	140	1
          *  *** *    *   **  **
MAP Score: 2.8887

Motif 9
CTCAAAGGGAGTGCATTCGGTACACTCGCCCGC          	2	0	0
GAGCAAGACAGCAGCACTGTACCCCTCACCCTGGATAGGAGCT	2	40	1
GAGCTCTAGAGCTATGCTATAGTCCCCGGCGGGGAGAGGCT  	2	78	1
CCTTTCTTCCTCATGCGCACTTCTCGCGCCAGCGAGCGTAACA	3	30	1
GCGGTAATCTGTCCAGCAAGGACACACGGACGCCTTGCGTACC	3	78	1
CGGACGCCTTGCGTACCCCAACCGCGAGCCTTGACAGAACATA	3	104	1
AGCCATGCCTCCTTCGACCAAACTCTCGGAGGGATGGATGATA	5	10	1
AAGCCTTTCTTCAGCTCTGTCGCACAAGGCAACTAACGCGCCG	5	81	1
AATGAGGACTGCACGCAAAACCTGCCAGGAAACAATGATGAGA	5	135	0
CAGTCCTCATTCAAGCAAAACGCCATCGGCGCCGAGAAGGGTC	5	167	1
          **      *   * * ****  *
MAP Score: 1.61971

Motif 10
AAGTCTCTTCTTCTTGGGGGAAGAGAGGGCAGAAAAGA	0	11	1
ACGTGTTCTATCTGTGGAGCGCGTTACGTTGGGTAGCG	0	75	1
ACGTTGGGTAGCGTAAGAGGGGGAGTGC          	0	100	1
     GGGTTGCGTACGGGTTAGATAAGAGCAGGAGCA	1	5	1
        GCGGGCGAGTGTACCGAATGCACTCCCTTT	2	2	1
CGAATGCACTCCCTTTGAGCAAGACAGCAGCACTGTAC	2	24	1
CTCCTATCCAGGGTGAGGGGTACAGTGCTGCTGTCTTG	2	43	0
CTATAGCATAGCTCTAGAGCTCCTATCCAGGGTGAGGG	2	62	0
  AGCCTCTCCCCGCCGGGGACTATAGCATAGCTCTAG	2	83	0
CGCGAGAAGTGCGCATGAGGAAGAAAGGACCACCCCGT	3	20	0
GGTACGCAAGGCGTCCGTGTGTCCTTGCTGGACAGATT	3	83	0
GTCAAGGCTCGCGGTTGGGGTACGCAAGGCGTCCGTGT	3	101	0
ATTGCGGAGGCCGATGGTGCGGTATTTGGGTATGTTCT	3	139	0
  GCTTTGCTCCTTACGAGATTGTTTGCAGAAAGTAG 	4	9	0
ACCAAACTCTCGGAGGGATGGATGATAGTACAGCGAAT	5	26	1
GCGCGTTAGTTGCCTTGTGCGACAGAGCTGAAGAAAGG	5	84	0
GACCCTTCTCGGCGCCGATGGCGTTTTGCTTGAATGAG	5	172	0
GCGCCGAGAAGGGTCCGATGAACAGATATACGTGTCGG	5	195	1
AACAGATATACGTGTCGGGGAGGTTTAC          	5	215	1
          ***   * *** *  * *
MAP Score: 1.56822

Motif 11
GCGGGCGAGTGTACCGAATGCACTCCCTTTGAGCAAGACAG	2	10	1
CAAGACAGCAGCACTGTACCCCTCACCCTGGATAGGAGCTC	2	43	1
 AGCCTCTCCCCGCCGGGGACTATAGCATAGCTCTAGAGCT	2	79	0
TTCCTCATGCGCACTTCTCGCGCCAGCGAGCGTAACACGCC	3	36	1
GACGCCTTGCGTACCCCAACCGCGAGCCTTGACAGAACATA	3	106	1
CCCAAATACCGCACCATCGGCCTCCGCAATGAGAAGGA   	3	147	1
   AGCCATGCCTCCTTCGACCAAACTCTCGGAGGGATGGA	5	7	1
CCTTTCTTCAGCTCTGTCGCACAAGGCAACTAACGCGCCGA	5	84	1
TCTGTTCATCGGACCCTTCTCGGCGCCGATGGCGTTTTGCT	5	180	0
          ** **     *   *** * *
MAP Score: 0.0337641