AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_profile008_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240598
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0185	147	signal peptidase I (sip)
#1	TP0186	54	oxygen-independent coproporphyrinogen III oxidase, putative
#2	TP0445	135	4-methyl-5(b-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme (thiJ)
#3	TP0446	41	gcpE protein (gcpE)
#4	TP0524	135	ATP-dependent protease LA (lon-2)
#5	TP0604	103	ribosome recycling factor

Motif 1
TCATTGCAAAGAACCGCAAGGCTTTTTTCA	0	18	0
GGCGCCATGAGGGGCACAGGAACCCATCTC	0	46	0
GCCCCTCATGGCGCCGGATGCTACCGGATA	0	61	1
TGCCGTGTCTGGGAGGGACGCCGTTTT   	0	130	1
   TGTGTAGGCGCCGCATTTGTGGTGCGT	1	7	1
ACAGCACGATGCGCAGCACGCACCACAAAT	1	24	0
  GATAAAAGGAACAGCACGATGCGCAGCA	1	36	0
CGCCCCGCGAGCGCAGCACTACCTTAGGAT	2	17	0
CTGCGCTCGCGGGGCGCACGGCTAGTACGT	2	31	1
TCGCTTTTGAACGGAGGACGATTATCCGTA	2	60	1
TCTGGCTGCCGCGCAGCACGCTCGTCCCTC	3	14	0
CCCGCAGGTCGTGCAAGACGTTTACTAGGA	4	27	0
ACGACCTGCGGGGGCGCAGTATACCGCGCA	4	45	1
GCAGTATACCGCGCAGGTATATTTTTTAAA	4	60	1
TAGTATCCAGGCAAGGGACGAAAAGTCAAT	4	107	0
        GTGGGAAGCACGGATAGATCCT	5	2	1
CCATCCTGCAGGGTGGCAGGATCTATCCGT	5	19	0
CCTGCAGGATGGGGAGCAAGCAGGCGTGGG	5	37	1
AGCAGGCGTGGGGGAGCTCGTGCTTCTCTC	5	55	1
TCACAACACAGTGCGGCAAGAGAGAAGCAC	5	74	0
          **********
MAP Score: 39.3445

Motif 2
AATGAGATGGGTTCCTGTGCCCCTCATGGCGCCGGATGCTAC	0	43	1
ATCGCCGTGTTAGGCTGCCGTGTCTGGGAGGGACGCCGTTTT	0	115	1
         TGTGTAGGCGCCGCATTTGTGGTGCGTGCTGCG	1	1	1
CGCATTTGTGGTGCGTGCTGCGCATCGTGCTGTTCCTTTTAT	1	21	1
TCTATCCTAAGGTAGTGCTGCGCTCGCGGGGCGCACGGCTAG	2	14	1
GGGGCGCACGGCTAGTACGTCGCTTTTGAACGGAGGACGATT	2	41	1
CTGTGTGCGCGGGGTTGCACTGTTGCTGTAAGAACAGGTACG	2	92	1
TCAGAGGGACGAGCGTGCTGCGCGGCAGCCAGAGGAAAAG  	3	11	1
ACCTGCGCGGTATACTGCGCCCCCGCAGGTCGTGCAAGACGT	4	36	0
AGCACGGATAGATCCTGCCACCCTGCAGGATGGGGAGCAAGC	5	16	1
GCGTGGGGGAGCTCGTGCTTCTCTCTTGCCGCACTGTGTTGT	5	60	1
          * *  ***  ***    *   *
MAP Score: 19.886

Motif 3
AATGAGATGGGTTCCTGTGCCCCTCATGGCGCCGGATGCTACCG	0	43	1
ATTCGATTATCGCCGTGTTAGGCTGCCGTGTCTGGGAGGGACGC	0	107	1
GCACGATGCGCAGCACGCACCACAAATGCGGCGCCTACACA   	1	7	0
TCTATCCTAAGGTAGTGCTGCGCTCGCGGGGCGCACGGCTAGTA	2	14	1
CCCCGTACCTGTTCTTACAGCAACAGTGCAACCCCGCGCACACA	2	93	0
TCAGAGGGACGAGCGTGCTGCGCGGCAGCCAGAGGAAAAG    	3	11	1
TCCTAGTAAACGTCTTGCACGACCTGCGGGGGCGCAGTATACCG	4	27	1
AGCACGGATAGATCCTGCCACCCTGCAGGATGGGGAGCAAGCAG	5	16	1
CCCCTCACAACACAGTGCGGCAAGAGAGAAGCACGAGCTCCCCC	5	64	0
          *  * ***  * *    *   * *
MAP Score: 12.4558

Motif 4
ATTGAAAAAAGCCTTGCGGTTCTTTGCAAT	0	16	1
TGTGCCCCTCATGGCGCCGGATGCTACCGG	0	58	1
TCGCCGTGTTAGGCTGCCGTGTCTGGGAGG	0	116	1
GTGTCTGGGAGGGACGCCGTTTT       	0	134	1
TTTGTGGTGCGTGCTGCGCATCGTGCTGTT	1	25	1
TCCTAAGGTAGTGCTGCGCTCGCGGGGCGC	2	18	1
CTGCGCTCGCGGGGCGCACGGCTAGTACGT	2	31	1
TGTGTGCGCGGGGTTGCACTGTTGCTGTAA	2	93	1
AGGGACGAGCGTGCTGCGCGGCAGCCAGAG	3	15	1
CCTAGTAAACGTCTTGCACGACCTGCGGGG	4	28	1
ACGACCTGCGGGGGCGCAGTATACCGCGCA	4	45	1
AGATCCTGCCACCCTGCAGGATGGGGAGCA	5	25	1
GGAGCAAGCAGGCGTGGGGGAGCTCGTGCT	5	49	1
TGCTTCTCTCTTGCCGCACTGTGTTGTGAG	5	75	1
          **********
MAP Score: 12.3099

Motif 5
ATGGGTTCCTGTGCCCCTCATGGCGCCGGATGCTACCGGATA	0	49	1
ATTCGATTATCGCCGTGTTAGGCTGCCGTGTCTGGGAGGGAC	0	107	1
TGCGCAGCACGCACCACAAATGCGGCGCCTACACA       	1	3	0
CTAGCCGTGCGCCCCGCGAGCGCAGCACTACCTTAGGATAGA	2	14	0
ATTATCCGTAGTCTGTGTGCGCGGGGTTGCACTGTTGCTGTA	2	80	1
GTTGCTGTAAGAACAGGTACGGGGGTGTTGCG          	2	113	1
TTTCCTCTGGCTGCCGCGCAGCACGCTCGTCCCTCTGAT   	3	7	0
GTATACTGCGCCCCCGCAGGTCGTGCAAGACGTTTACTAGGA	4	27	0
TTTTTTAAAAGGCCTCGAATGGAGGCATTGACTTTTCGTCCC	4	81	1
      AGGGCGCCTAGTATCCAGGCAAGGGACGAAAAGTCA	4	109	0
GCTTGCTCCCCATCCTGCAGGGTGGCAGGATCTATCCGTGCT	5	16	0
AGAAGCACGAGCTCCCCCACGCCTGCTTGCTCCCCATCCTGC	5	40	0
GGGAGCTCGTGCTTCTCTCTTGCCGCACTGTGTTGTGAGGGG	5	66	1
          *  ** *   **  **  *  *
MAP Score: 11.4913

Motif 6
TCTATCCTAAGGTAGTGCTGCGCTCGCGGGGCGCACGGCTAGTACGTCG	2	14	1
       TGTGTAGGCGCCGCATTTGTGGTGCGTGCTGCGCATCGTGCT	1	3	1
CCCCGTACCTGTTCTTACAGCAACAGTGCAACCCCGCGCACACAGACTA	2	88	0
GTTCTTTGCAATGAGATGGGTTCCTGTGCCCCTCATGGCGCCGGATGCT	0	34	1
       GTGGGAAGCACGGATAGATCCTGCCACCCTGCAGGATGGGGA	5	3	1
TAAACGTCTTGCACGACCTGCGGGGGCGCAGTATACCGCGCAGGTATAT	4	33	1
   ATCAGAGGGACGAGCGTGCTGCGCGGCAGCCAGAGGAAAAG     	3	7	1
CGCCGTGTTAGGCTGCCGTGTCTGGGAGGGACGCCGTTTT         	0	117	1
GCGTGGGGGAGCTCGTGCTTCTCTCTTGCCGCACTGTGTTGTGAGGGGA	5	60	1
CATGGCGCCGGATGCTACCGGATAGGCACTTCCCTTGTCAATTCGATTA	0	67	1
          *   *  * *     * *   * *   **
MAP Score: 10.714

Motif 7
GCCGTGTTAGGCTGCCGTGTCTGGGAGGGACGCCG	0	118	1
CTAAGGTAGTGCTGCGCTCGCGGGGCGCACGGCTA	2	20	1
TGTGCGCGGGGTTGCACTGTTGCTGTAAGAACAGG	2	95	1
GGACGAGCGTGCTGCGCGGCAGCCAGAGGAAAAG 	3	17	1
TGCGCGGTATACTGCGCCCCCGCAGGTCGTGCAAG	4	40	0
TGCTCCCCATCCTGCAGGGTGGCAGGATCTATCCG	5	20	0
GGGAGCTCGTGCTTCTCTCTTGCCGCACTGTGTTG	5	66	1
          ***** * *  ** *
MAP Score: 9.75846

Motif 8
CCGGTAGCATCCGGCGCCATGAGGGGCACAGGAACCCATC	0	48	0
GGCGCCGGATGCTACCGGATAGGCACTTCCCTTGTCAATT	0	70	1
CCCAGACACGGCAGCCTAACACGGCGATAATCGAATTGAC	0	103	0
    TGTGTAGGCGCCGCATTTGTGGTGCGTGCTGCGCAT	1	6	1
GATAAAAGGAACAGCACGATGCGCAGCACGCACCACAAAT	1	24	0
ATCCTAAGGTAGTGCTGCGCTCGCGGGGCGCACGGCTAGT	2	17	1
GCGCTCGCGGGGCGCACGGCTAGTACGTCGCTTTTGAACG	2	33	1
TCCTCTGGCTGCCGCGCAGCACGCTCGTCCCTCTGAT   	3	7	0
TAGTAAACGTCTTGCACGACCTGCGGGGGCGCAGTATACC	4	30	1
GACCTGCGGGGGCGCAGTATACCGCGCAGGTATATTTTTT	4	47	1
ATCCTGCCACCCTGCAGGATGGGGAGCAAGCAGGCGTGGG	5	27	1
CTTCTCTCTTGCCGCACTGTGTTGTGAGGGGAAAAG    	5	77	1
          ** ** * **  *  *   *
MAP Score: 9.26573

Motif 9
GCGGTTCTTTGCAATGAGATGGGTTCCTGTGCCCCTCATGGCGCC	0	31	1
GCCGTGTTAGGCTGCCGTGTCTGGGAGGGACGCCGTTTT      	0	118	1
 TGTGTAGGCGCCGCATTTGTGGTGCGTGCTGCGCATCGTGCTGT	1	9	1
CGACGTACTAGCCGTGCGCCCCGCGAGCGCAGCACTACCTTAGGA	2	18	0
ACGATTATCCGTAGTCTGTGTGCGCGGGGTTGCACTGTTGCTGTA	2	77	1
TTGCACTGTTGCTGTAAGAACAGGTACGGGGGTGTTGCG      	2	106	1
    ATCAGAGGGACGAGCGTGCTGCGCGGCAGCCAGAGGAAAAG	3	6	1
GACCTGCGGGGGCGCAGTATACCGCGCAGGTATATTTTTTAAAAG	4	47	1
        AGGGCGCCTAGTATCCAGGCAAGGGACGAAAAGTCAA	4	108	0
      GTGGGAAGCACGGATAGATCCTGCCACCCTGCAGGATGG	5	4	1
TGCAGGATGGGGAGCAAGCAGGCGTGGGGGAGCTCGTGCTTCTCT	5	39	1
          *  **  *    *   * *  ** *
MAP Score: 8.62592

Motif 10
TTCGATTATCGCCGTGTTAGGCTGCCGTGTCTGGGAGGGAC	0	108	1
   TGTGTAGGCGCCGCATTTGTGGTGCGTGCTGCGCATCG	1	7	1
TCCTAAGGTAGTGCTGCGCTCGCGGGGCGCACGGCTAGTAC	2	18	1
CACGGCTAGTACGTCGCTTTTGAACGGAGGACGATTATCCG	2	47	1
TGTGTGCGCGGGGTTGCACTGTTGCTGTAAGAACAGGTACG	2	93	1
      ATCAGAGGGACGAGCGTGCTGCGCGGCAGCCAGAG	3	4	1
CCTAGTAAACGTCTTGCACGACCTGCGGGGGCGCAGTATAC	4	28	1
TTTTTAAAAGGCCTCGAATGGAGGCATTGACTTTTCGTCCC	4	82	1
        GTGGGAAGCACGGATAGATCCTGCCACCCTGCA	5	2	1
CCTGCAGGATGGGGAGCAAGCAGGCGTGGGGGAGCTCGTGC	5	37	1
TCACAACACAGTGCGGCAAGAGAGAAGCACGAGCTCCCCCA	5	63	0
          * *  **  *   ** * * *
MAP Score: 7.49274

Motif 11
CAATGAGATGGGTTCCTGTGCCCCTCATGG	0	42	1
CGCCGTGTTAGGCTGCCGTGTCTGGGAGGG	0	117	1
TGCCGTGTCTGGGAGGGACGCCGTTTT   	0	130	1
GGCGCCGCATTTGTGGTGCGTGCTGCGCAT	1	16	1
TATCCTAAGGTAGTGCTGCGCTCGCGGGGC	2	16	1
AGTGCTGCGCTCGCGGGGCGCACGGCTAGT	2	27	1
CGGGGCGCACGGCTAGTACGTCGCTTTTGA	2	40	1
ACAGGTACGGGGGTGTTGCG          	2	125	1
    ATCAGAGGGACGAGCGTGCTGCGCGG	3	6	1
CTTTTCCTCTGGCTGCCGCGCAGCACGCTC	3	21	0
GCGCCCCCGCAGGTCGTGCAAGACGTTTAC	4	32	0
TAGTATCCAGGCAAGGGACGAAAAGTCAAT	4	107	0
        GTGGGAAGCACGGATAGATCCT	5	2	1
CCATCCTGCAGGGTGGCAGGATCTATCCGT	5	19	0
TGCGGCAAGAGAGAAGCACGAGCTCCCCCA	5	63	0
          **********
MAP Score: 0.225509