AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons016_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239460
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0051	150	peptide chain release factor 1 (prfA)
#1	TP0255	118	ribosomal protein L31 (rpmE)
#2	TP0474	140	conserved hypothetical protein
#3	TP0576	300	peptide chain release factor 2 (prfB)

Motif 1
      GTTAGCCTCTCCTGCACGAGCACGAAAACA	0	4	1
TTTTTTAGCATCATGGCAAGCTCTTTTTCTATTCGT	0	55	1
CTTTTTCTATTCGTGTCGTGGCCTGGAACTGTCTTT	0	77	1
CTGAATATTTTATGCTCCTGCGCGAGGGCCCCC   	0	127	1
CTTCCAGAAGGCTCGTACACGCCGGGTGTAACCGAC	1	30	0
CCATTCTACAGCGCGCCGCGCCCTTAAAAAGGTTAC	1	75	0
    GTCTGTGCTTCTTAAGCCCGCGGTAATTACGC	2	6	1
CGCTGGCGCATATTGCACGGCCCGCGTAATTACCGC	2	29	0
CGTGCAATATGCGCCAGCGGGACTTGGAGAAAAGCG	2	46	1
CCTGATGCTAGCACGGTGTGCGCTTTTCTCCAAGTC	2	66	0
CACCGTGCTAGCATCAGGCGCCCGCGTTCCGGTACG	2	84	1
  GAGATCTTTCCCCTAATGCCCGAAAATGTACGTA	2	116	0
TTCTGGCGGGGCTCGGCCTGCGAGCGTTGAGTGTGC	3	17	1
AGACTGAAATGCGTGATAAGAACGTGTGCAGCGTCT	3	68	0
CTCTGATGCAGAGCACTGTGCACGTGCAGCCGTGCA	3	102	1
CAGGTATTACGCTTGAGAAAGACGAGGAAGAACCCT	3	191	1
AACGCCTGAGGCCTCCTCCGCTATGGGGATCGAGGG	3	231	0
          ** **  * ** ** *
MAP Score: 22.9972

Motif 2
GCACACTCAACGCTCGCAGGCCGAGCCCCGCCAGAAG	3	16	0
TGGAGAAAAGCGCACACCGTGCTAGCATCAGGCGCCC	2	70	1
GTCGGTTACACCCGGCGTGTACGAGCCTTCTGGAAGA	1	30	1
GTGCAATATGCGCCAGCGGGACTTGGAGAAAAGCGCA	2	47	1
TCTGATGCAGAGCACTGTGCACGTGCAGCCGTGCAGC	3	103	1
GCCTTCTTCACGCATCGAGACGCTGCACACGTTCTTA	3	51	1
CTTTCAGATGCGCAGTCAGTCCGCACACTCATCGAAG	3	139	1
     GTTAGCCTCTCCTGCACGAGCACGAAAACACC	0	5	1
TTTTTAAGGGCGCGGCGCGCTGTAGAATGGGGAAAGG	1	81	1
CCCCTCGATCCCCATAGCGGAGGAGGCCTCAGGCGTT	3	230	1
TTTTTCTATTCGTGTCGTGGCCTGGAACTGTCTTTGT	0	78	1
      GGGGGCCCTCGCGCAGGAGCATAAAATATTC	0	129	0
GCCCGCGGTAATTACGCGGGCCGTGCAATATGCGCCA	2	25	1
AAATGTACGTACCGGAACGCGGGCGCCTGATGCTAGC	2	90	0
 GAGATCTTTCCCCTAATGCCCGAAAATGTACGTACC	2	114	0
          ***   * *  ** ***
MAP Score: 22.2918

Motif 3
TTGGAGAAAAGCGCACACCGTGCTAGCATCAGG	2	69	1
CCATTCTACAGCGCGCCGCGCCCTTAAAAAGGT	1	78	0
CGCGGTAATTACGCGGGCCGTGCAATATGCGCC	2	28	1
TCTTCTGGCGGGGCTCGGCCTGCGAGCGTTGAG	3	15	1
AAGAACATCTGCGCACCGCAGGTATTACGCTTG	3	173	1
CTGATGCAGAGCACTGTGCACGTGCAGCCGTGC	3	104	1
TGTGTCGGTTACACCCGGCGTGTACGAGCCTTC	1	27	1
CTAGCATCAGGCGCCCGCGTTCCGGTACGTACA	2	91	1
CGTGAAGAAGGCACACTCAACGCTCGCAGGCCG	3	30	0
ACGCATCGAGACGCTGCACACGTTCTTATCACG	3	60	1
GCTTTCAGATGCGCAGTCAGTCCGCACACTCAT	3	138	1
ACGAGGAAGAACCCTCACCCCCTCGATCCCCAT	3	212	1
GAGCACGAAAACACCCTACATCTAATGCTTTTT	0	27	1
CAGTCAGTCCGCACACTCATCGAAGAACATCTG	3	151	1
TTATGCTCCTGCGCGAGGGCCCCC         	0	136	1
          **** * ** ***
MAP Score: 17.4919

Motif 4
CCATTCTACAGCGCGCCGCGCCCTTAAAAAGGT	1	78	0
TTATGCTCCTGCGCGAGGGCCCCC         	0	136	1
      GTTAGCCTCTCCTGCACGAGCACGAAA	0	4	1
AACGCTCGCAGGCCGAGCCCCGCCAGAAGAAAG	3	12	0
CACCGTGCTAGCATCAGGCGCCCGCGTTCCGGT	2	84	1
CGTGCAATATGCGCCAGCGGGACTTGGAGAAAA	2	46	1
CAAGCGTAATACCTGCGGTGCGCAGATGTTCTT	3	173	0
GGCGCATATTGCACGGCCCGCGTAATTACCGCG	2	28	0
AAAACGCCTGAGGCCTCCTCCGCTATGGGGATC	3	236	0
CGTGATAAGAACGTGTGCAGCGTCTCGATGCGT	3	60	0
GTGCACGTGCAGCCGTGCAGCTTTCAGATGCGC	3	119	1
CCTGATGCTAGCACGGTGTGCGCTTTTCTCCAA	2	69	0
CGAGGAAGAACCCTCACCCCCTCGATCCCCATA	3	213	1
TGTCGGTTACACCCGGCGTGTACGAGCCTTCTG	1	29	1
          ***** ** ** *
MAP Score: 15.5776

Motif 5
TTCGTGTCGTGGCCTGGAACTGTCTTTGTTGAAAGCTTCGCCTGA	0	86	1
TGTGTCGGTTACACCCGGCGTGTACGAGCCTTCTGGAAGAGGGTG	1	27	1
ACCTTTTTAAGGGCGCGGCGCGCTGTAGAATGGGGAAAGGAGCGA	1	78	1
GGCGCATATTGCACGGCCCGCGTAATTACCGCGGGCTTAAGAAGC	2	16	0
TTGGAGAAAAGCGCACACCGTGCTAGCATCAGGCGCCCGCGTTCC	2	69	1
TCTTCTGGCGGGGCTCGGCCTGCGAGCGTTGAGTGTGCCTTCTTC	3	15	1
CGTTGAGTGTGCCTTCTTCACGCATCGAGACGCTGCACACGTTCT	3	41	1
CTGATGCAGAGCACTGTGCACGTGCAGCCGTGCAGCTTTCAGATG	3	104	1
GCTTTCAGATGCGCAGTCAGTCCGCACACTCATCGAAGAACATCT	3	138	1
AAGAACATCTGCGCACCGCAGGTATTACGCTTGAGAAAGACGAGG	3	173	1
ACGAGGAAGAACCCTCACCCCCTCGATCCCCATAGCGGAGGAGGC	3	212	1
          **** *  * ***           *
MAP Score: 10.9964

Motif 6
         GGGGGCCCTCGCGCAGGAGCATAA	0	136	0
TAACCTTTTTAAGGGCGCGGCGCGCTGTAGAAT	1	76	1
CGCGGTAATTACGCGGGCCGTGCAATATGCGCC	2	28	1
TTTTCTCCAAGTCCCGCTGGCGCATATTGCACG	2	46	0
ACTTGGAGAAAAGCGCACACCGTGCTAGCATCA	2	67	1
AACGCTCGCAGGCCGAGCCCCGCCAGAAGAAAG	3	12	0
CGTGATAAGAACGTGTGCAGCGTCTCGATGCGT	3	60	0
GCACGGCTGCACGTGCACAGTGCTCTGCATCAG	3	104	0
GTGCACGTGCAGCCGTGCAGCTTTCAGATGCGC	3	119	1
ATCGAAGAACATCTGCGCACCGCAGGTATTACG	3	169	1
AAAACGCCTGAGGCCTCCTCCGCTATGGGGATC	3	236	0
          * *** ** ****
MAP Score: 9.5443

Motif 7
CGCCGGGTGTAACCGACACACGTTCCAGTCTC	1	15	0
GAAGGCTCGTACACGCCGGGTGTAACCGACAC	1	28	0
ACCTTTTTAAGGGCGCGGCGCGCTGTAGAATG	1	78	1
CGCGGTAATTACGCGGGCCGTGCAATATGCGC	2	28	1
CCTGATGCTAGCACGGTGTGCGCTTTTCTCCA	2	70	0
AAAATGTACGTACCGGAACGCGGGCGCCTGAT	2	96	0
TTCTGGCGGGGCTCGGCCTGCGAGCGTTGAGT	3	17	1
GTGTGCAGCGTCTCGATGCGTGAAGAAGGCAC	3	49	0
ACGCATCGAGACGCTGCACACGTTCTTATCAC	3	60	1
CTGATGCAGAGCACTGTGCACGTGCAGCCGTG	3	104	1
ATGAGTGTGCGGACTGACTGCGCATCTGAAAG	3	139	0
CAAGCGTAATACCTGCGGTGCGCAGATGTTCT	3	174	0
          ** *** *****
MAP Score: 7.74684

Motif 8
GTGTCGGTTACACCCGGCGTGTACGAGCCTTCTGGAAGAGGGTG	1	28	1
CCTTTTTAAGGGCGCGGCGCGCTGTAGAATGGGGAAAGGAGCGA	1	79	1
TAATTACGCGGGCCGTGCAATATGCGCCAGCGGGACTTGGAGAA	2	33	1
GAAAAGCGCACACCGTGCTAGCATCAGGCGCCCGCGTTCCGGTA	2	74	1
TCTTTCTTCTGGCGGGGCTCGGCCTGCGAGCGTTGAGTGTGCCT	3	11	1
TGATGCAGAGCACTGTGCACGTGCAGCCGTGCAGCTTTCAGATG	3	105	1
AGAACATCTGCGCACCGCAGGTATTACGCTTGAGAAAGACGAGG	3	174	1
          *** * **  *     *    * *
MAP Score: 6.28886

Motif 9
TGTCGGTTACACCCGGCGTGTACGAGCCTTCTG	1	29	1
CTTTTTAAGGGCGCGGCGCGCTGTAGAATGGGG	1	80	1
CGCGGTAATTACGCGGGCCGTGCAATATGCGCC	2	28	1
CGTGCAATATGCGCCAGCGGGACTTGGAGAAAA	2	46	1
CCTGATGCTAGCACGGTGTGCGCTTTTCTCCAA	2	69	0
CTTTCTTCTGGCGGGGCTCGGCCTGCGAGCGTT	3	12	1
GCATCGAGACGCTGCACACGTTCTTATCACGCA	3	62	1
AAGCTGCACGGCTGCACGTGCACAGTGCTCTGC	3	109	0
GCTTTCAGATGCGCAGTCAGTCCGCACACTCAT	3	138	1
GAACATCTGCGCACCGCAGGTATTACGCTTGAG	3	175	1
GATCCCCATAGCGGAGGAGGCCTCAGGCGTTTT	3	236	1
          *******  ** *
MAP Score: 4.9972

Motif 10
GAAGGCTCGTACACGCCGGGTGTAACCGACACA	1	27	0
ACCTTTTTAAGGGCGCGGCGCGCTGTAGAATGG	1	78	1
CCCGCGGTAATTACGCGGGCCGTGCAATATGCG	2	26	1
ACTTGGAGAAAAGCGCACACCGTGCTAGCATCA	2	67	1
TGCTAGCATCAGGCGCCCGCGTTCCGGTACGTA	2	89	1
TCTTCTGGCGGGGCTCGGCCTGCGAGCGTTGAG	3	15	1
ACGGCTGCACGTGCACAGTGCTCTGCATCAGAG	3	102	0
CAGCTTTCAGATGCGCAGTCAGTCCGCACACTC	3	136	1
AATACCTGCGGTGCGCAGATGTTCTTCGATGAG	3	166	0
TAGCGGAGGAGGCCTCAGGCGTTTTCTCCATAC	3	244	1
          * ****** * **
MAP Score: 2.98899

Motif 11
         GGGGGCCCTCGCGCAGGAGCA	0	139	0
TGTCGGTTACACCCGGCGTGTACGAGCCTT	1	29	1
CTTTTTAAGGGCGCGGCGCGCTGTAGAATG	1	80	1
GGCGCATATTGCACGGCCCGCGTAATTACC	2	31	0
ATATGCGCCAGCGGGACTTGGAGAAAAGCG	2	52	1
CCTGATGCTAGCACGGTGTGCGCTTTTCTC	2	72	0
AATGTACGTACCGGAACGCGGGCGCCTGAT	2	96	0
CTTTCTTCTGGCGGGGCTCGGCCTGCGAGC	3	12	1
CTGATGCAGAGCACTGTGCACGTGCAGCCG	3	104	1
CGTAATACCTGCGGTGCGCAGATGTTCTTC	3	172	0
ATGGGGATCGAGGGGGTGAGGGTTCTTCCT	3	215	0
          **********
MAP Score: 1.30656

Motif 12
GTGTTTTCGTGCTCGTGCAGGAGAGGCTAAC      	0	4	0
AATATTTTATGCTCCTGCGCGAGGGCCCCC       	0	130	1
CTTCCAGAAGGCTCGTACACGCCGGGTGTAACCGACA	1	29	0
CTTTTTAAGGGCGCGGCGCGCTGTAGAATGGGGAAAG	1	80	1
CGCGGTAATTACGCGGGCCGTGCAATATGCGCCAGCG	2	28	1
TCTCCAAGTCCCGCTGGCGCATATTGCACGGCCCGCG	2	39	0
TTGGAGAAAAGCGCACACCGTGCTAGCATCAGGCGCC	2	69	1
ACGTACCGGAACGCGGGCGCCTGATGCTAGCACGGTG	2	84	0
TCTTCTGGCGGGGCTCGGCCTGCGAGCGTTGAGTGTG	3	15	1
TGCGTGAAGAAGGCACACTCAACGCTCGCAGGCCGAG	3	28	0
CTGCACGGCTGCACGTGCACAGTGCTCTGCATCAGAG	3	102	0
GCTTTCAGATGCGCAGTCAGTCCGCACACTCATCGAA	3	138	1
GAGGAAGAACCCTCACCCCCTCGATCCCCATAGCGGA	3	214	1
ACGCCTGAGGCCTCCTCCGCTATGGGGATCGAGGGGG	3	229	0
          **** * * *   * **
MAP Score: 0.761832