AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons033_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243107
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	gcpE	151	hypothetical protein
#1	yceC	46	predicted pseudouridine synthetase family
#2	CT656	300	hypothetical protein
#3	sfhB	83	(Pseudouridine Synthase)
#4	cafE	300	Axial Filament Protein

Motif 1
CTTATACTTCCTCAGCCCCCCAAAACCTTTA	0	65	1
TCTGGAAGCACTCTTCCTTCTTCTATTCCTT	2	44	0
TGGATAGAGCATCCGCCTTCTAAGCGGATGG	2	146	1
TTCAGATTTTATCTCCTTTCTCTCGTGAAAA	2	223	1
CAGCATAAGGAACAGCCTTCTTATCCTGTCG	4	33	1
CTTGTTGGCAATCCGCTTTCCTTGTGTTTCG	4	72	0
TCGACTTATAATCCGCCTTCTGCTTAATAAA	4	209	1
TTTAAAATAACTCCCCATCCTCGGAATCAGG	4	241	1
TTCCTAAATGCTCTGCGCTCTACAGGAGTCC	4	275	0
          ****** ****
MAP Score: 10.8491

Motif 2
GGCCGAATCTCTTTCTCCTAAAGGTTTTGG	0	84	0
       AGAAATTCTCGTAAAATCGTACC	1	3	1
TCAAACTGCTAATCCGCCGAATC       	2	3	0
TGGAAGCACTCTTCCTTCTTCTATTCCTTG	2	43	0
GTGGATAGAGCATCCGCCTTCTAAGCGGAT	2	145	1
AACCTGCGACCATCCGCTTAGAAGGCGGAT	2	156	0
GTCCGAGACACATGCTTCTTTCTTTTCAGA	2	199	1
         CAAGCCTCCTTAAAACAGGAC	3	72	0
GCATAAGGAACAGCCTTCTTATCCTGTCGC	4	35	1
TCTTGTTGGCAATCCGCTTTCCTTGTGTTT	4	74	0
ATTCTACAAAAATGCTTGTTGTTGAATAGT	4	168	0
ATCGACTTATAATCCGCCTTCTGCTTAATA	4	208	1
AATAACTCCCCATCCTCGGAATCAGGTGAG	4	246	1
          **********
MAP Score: 10.5877

Motif 3
AACAATTTTTGAAATTGGCTGGGACAGTACC	0	114	0
CACACTTATCGATAATGGATT          	1	35	1
TCAAGGAATAGAAGAAGGAAGAGTGCTTCCA	2	42	1
AGTGCTTCCAGAAAATCGAAGTCTAAGGTAT	2	63	1
CATCCGCTTAGAAGGCGGATGCTCTATCCAC	2	145	0
CTTCTAAGCGGATGGTCGCAGGTTCGAATCC	2	162	1
AATCTGAAAAGAAAGAAGCATGTGTCTCGGA	2	200	0
   CGGTTTGGAAGGTTGAATAAATCTTTTC	3	7	1
AGTCCTGTTTTAAGGAGGCTTG         	3	71	1
AGCGACAGGATAAGAAGGCTGTTCCTTATGC	4	35	0
GAAACACAAGGAAAGCGGATTGCCAACAAGA	4	73	1
TTATTAAGCAGAAGGCGGATTATAAGTCGAT	4	208	0
          ***** *****
MAP Score: 9.47922

Motif 4
AGCTTTAGATCAATTTAAAGGAAGGTCTCCATG	0	34	0
GTTTGAACAAGCATCTCAAGGAATAGAAGAAGG	2	27	1
CCAGAAAATCGAAGTCTAAGGTATAGTATCTTC	2	70	1
TAGTATCTTCCAGCACTATGGAAGTGTTTCCTT	2	93	1
AGCTATCGGTCCACAGCAAGGAAACACTTCCAT	2	110	0
CTTTTCCGAACCGTATCATGGAAGGGTTTCAAA	3	32	1
AAAAGTGTTTGCAGCATAAGGAACAGCCTTCTT	4	22	1
GCTGAGCAACGAAACACAAGGAAAGCGGATTGC	4	63	1
GTAGAGCGCAGAGCATTTAGGAACGCC      	4	283	1
          ***   *******
MAP Score: 7.67043

Motif 5
AACCTTTAGGAGAAAGAGATTCGGCCGGTACTGTCCC	0	88	1
         GATTCGGCGGATTAGCAGTTTGAACAAG	2	1	1
TTGAACAAGCATCTCAAGGAATAGAAGAAGGAAGAGT	2	29	1
AGAAAATCGAAGTCTAAGGTATAGTATCTTCCAGCAC	2	72	1
AGGAGATAAAATCTGAAAAGAAAGAAGCATGTGTCTC	2	203	0
AAAAGTATTTTTCACGAGAGAAAGGAGATAAAATCTG	2	225	0
AAACCCTTCCATGATACGGTTCGGAAAAGATTTATTC	3	24	0
TTCGTTGCTCAGCGACAGGATAAGAAGGCTGTTCCTT	4	39	0
ATTGCCAACAAGAATAAGAGTTGGCAGTTGTCACTAT	4	91	1
AAGGCGGATTATAAGTCGATTAGGTAAAAAATTCTAC	4	191	0
TCCTCACCTGATTCCGAGGATGGGGAGTTATTTTAAA	4	241	0
          **    *** * ** **
MAP Score: 4.52383

Motif 6
CCAAAACCTTTAGGAGAAAGAGATTCGGCCGG	0	84	1
ACAAGCATCTCAAGGAATAGAAGAAGGAAGAG	2	33	1
AGAGTGCTTCCAGAAAATCGAAGTCTAAGGTA	2	61	1
GCTATCGGTCCACAGCAAGGAAACACTTCCAT	2	110	0
ACCGATAGCTCAGTGGATAGAGCATCCGCCTT	2	133	1
GATAAAATCTGAAAAGAAAGAAGCATGTGTCT	2	204	0
TATTTTTCACGAGAGAAAGGAGATAAAATCTG	2	225	0
GAGACTCCCCCAATACAAAGATTTTTCTGTAT	2	274	0
AAAGTGTTTGCAGCATAAGGAACAGCCTTCTT	4	23	1
TGCTCAGCGACAGGATAAGAAGGCTGTTCCTT	4	39	0
CTGAGCAACGAAACACAAGGAAAGCGGATTGC	4	64	1
GGATTGCCAACAAGAATAAGAGTTGGCAGTTG	4	89	1
ATAGAAATCACAATAAAAGAAACAAATCAGTT	4	126	1
          *** * ******
MAP Score: 2.89888