AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons033_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243121
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	gcpE	151	hypothetical protein
#1	CT058	79	hypothetical protein
#2	fer	181	Ferredoxin
#3	yceC	46	predicted pseudouridine synthetase family
#4	CT656	300	hypothetical protein
#5	sfhB	83	(Pseudouridine Synthase)
#6	cafE	300	Axial Filament Protein

Motif 1
CAAAACCTTTAGGAGAAAGAGATTCGGCCGG	0	85	1
AAAAATTTTAAAAGTTAAGAGTTT       	1	65	1
TATACTAGACAAGAGAAAGATACTGTAA   	2	7	0
TCCGATTTAAAAAAGTAGGAGCTAAGGAAGT	2	52	0
AAGATTAGTTAAGAATCGGAGTAGAGGGATT	2	138	0
CTCCAGAAGGAAAAAGAAAAGATTAGTTAAG	2	156	0
AAGCATCTCAAGGAATAGAAGAAGGAAGAGT	4	35	1
CCATCCGCTTAGAAGGCGGATGCTCTATCCA	4	146	0
CGGACCGAGCAGGATTCGAACCTGCGACCAT	4	173	0
TAAAATCTGAAAAGAAAGAAGCATGTGTCTC	4	203	0
ATTTTTCACGAGAGAAAGGAGATAAAATCTG	4	225	0
GAAGGGTTTCAAAAGACGAAGTCCTGTTTTA	5	52	1
GCTCAGCGACAGGATAAGAAGGCTGTTCCTT	6	39	0
GATTGCCAACAAGAATAAGAGTTGGCAGTTG	6	90	1
ATCACAATAAAAGAAACAAATCAGTTTCTAA	6	132	1
TTTATTAAGCAGAAGGCGGATTATAAGTCGA	6	209	0
CCTGATTCCGAGGATGGGGAGTTATTTTAAA	6	241	0
GGACTCCTGTAGAGCGCAGAGCATTTAGGAA	6	275	1
          **** ******
MAP Score: 10.4689

Motif 2
 ACAATTTTTAAAGGGAAGTTTCTCCATGG	0	9	1
GTTCTTGCGCAAAACGGTGTGTTGTCCTTT	1	25	1
CTACTTTTTTAAATCGGAGTATAGCGCAGC	2	65	1
GATTAGTTAAGAATCGGAGTAGAGGGATTC	2	137	0
TGCTTCCAGAAAATCGAAGTCTAAGGTATA	4	65	1
ATCCGCTTAGAAGGCGGATGCTCTATCCAC	4	145	0
ATCCGCCTTCTAAGCGGATGGTCGCAGGTT	4	156	1
AGGGTTTCAAAAGACGAAGTCCTGTTTTAA	5	54	1
AAACACAAGGAAAGCGGATTGCCAACAAGA	6	74	1
TATTAAGCAGAAGGCGGATTATAAGTCGAT	6	208	0
          **********
MAP Score: 8.79579

Motif 3
CTGTCCCAGCCAATTTCAAAAATTGTTTGTA	0	118	1
AGAAACAAATCAGTTTCTAAATTAAACTATT	6	143	1
         ACAATTTTTAAAGGGAAGTTTC	0	1	1
CGCTATACTCCGATTTAAAAAAGTAGGAGCT	2	60	0
TCTTGGGCAAAAATTTTAAAAGTTAAGAGTT	1	57	1
TCTGCTTAATAAATTTTAAAATAACTCCCCA	6	227	1
GGCGGATTAGCAGTTTGAACAAGCATCTCAA	4	15	1
         TAAGTTTTTAAAAAAAGTGTTT	6	1	1
TATCATGGAAGGGTTTCAAAAGACGAAGTCC	5	45	1
AAAGGAGATAAAATCTGAAAAGAAAGAAGCA	4	211	0
          ****** ****
MAP Score: 8.51168

Motif 4
CTAAAGGTTTTGGGGGGCTGAGGAAGTATA	0	67	0
AGAATCGGAGTAGAGGGATTCGAACCCCCG	2	128	0
       GATTCGGCGGATTAGCAGTTTGA	4	3	1
ATCCGCTTAGAAGGCGGATGCTCTATCCAC	4	145	0
ATCCGCCTTCTAAGCGGATGGTCGCAGGTT	4	156	1
GTCCTGTTTTAAGGAGGCTTG         	5	72	1
GCGACAGGATAAGAAGGCTGTTCCTTATGC	6	35	0
AAACACAAGGAAAGCGGATTGCCAACAAGA	6	74	1
TATTAAGCAGAAGGCGGATTATAAGTCGAT	6	208	0
          **********
MAP Score: 8.30619

Motif 5
TTTTAAAGGGAAGTTTCTCCATGGAGACCT	0	15	1
CAATTTCAAAAATTGTTTGTAGGACACCTC	0	128	1
TAACTTTTAAAATTTTTGCCCAAGAGCAAA	1	52	0
ATTCTTAACTAATCTTTTCTTTTTCCTTCT	2	153	1
AGCACTATGGAAGTGTTTCCTTGCTGTGGA	4	104	1
AGGTTGAATAAATCTTTTCCGAACCGTATC	5	19	1
TTTTTAAAAAAAGTGTTTGCAGCATAAGGA	6	14	1
TTAGAAACTGATTTGTTTCTTTTATTGTGA	6	133	0
ATTTTTGTAGAATTTTTTACCTAATCGACT	6	185	1
          **********
MAP Score: 2.22128

Motif 6
AAAGGAAGGTCTCCATGGAGAAACTTCCCTTTA	0	18	0
TTGTCCTTTGCTCTTGGGCAAAAATTTTAAAAG	1	46	1
GAACAAGCATCTCAAGGAATAGAAGAAGGAAGA	4	31	1
GGACCGATAGCTCAGTGGATAGAGCATCCGCCT	4	131	1
TATCTCCTTTCTCTCGTGAAAAATACTTTTGAC	4	232	1
ATACTTTTGACTCAAGTAAAATACAGAAAAATC	4	254	1
          ***  **** ***
MAP Score: 0.445256