AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i242_hfl_operon_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0151 109 hflK protein (hflK) #2 HI0152 300 H. influenzae predicted coding region HI0152 Motif number 1 GATTTTATATAAGGATTTTTTTGA 1 5 0 AAGGATTTTT 0.987303 -105 ATATAAAATCAAGGATTTTTTATTGCCTAA 1 25 1 AAGGATTTTT 0.987303 -85 ATGAAAATACAAGGCTTTTTAGGCAATAAA 1 43 0 AAGGCTTTTT 0.974602 -67 AAAAATTGTTAAGAGTTTAGCTAAATAAAT 1 84 0 AAGAGTTTAG 0.845426 -26 CTAAACTCTTAACAATTTTTTGACAA 1 94 1 AACAATTTTT 0.890451 -16 AATAATATTTACCAATTTTTGTTGTACCCG 2 133 0 ACCAATTTTT 0.865035 -168 TTTATATTAAAAGGATTTAGTTTGTGTGTA 2 254 0 AAGGATTTAG 0.968641 -47 ********** Masking position 1 Map Score: 7.89161 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 244 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 2 AATCAAGGATTTTTTATTGCCTAAAAAGCC 1 31 1 TTTTTATTGC 0.909671 -79 TTTAGCTAAATAAATGGGGCACGTCTATGA 1 69 0 TAAATGGGGC 0.88865 -41 ACGTCAAAGTTTACTGTTGCAATATCTGAC 2 101 0 TTACTGTTGC 0.986801 -200 TATTTACCAATTTTTGTTGTACCCGTTACG 2 128 0 TTTTTGTTGT 0.909671 -173 TAACCACAGTTTTATGGTGCCAGGTTTAAT 2 164 1 TTTATGGTGC 0.988814 -137 TTAATTGGGGTTGTTGTTGCTTGCTTGGTC 2 189 1 TTGTTGTTGC 0.975976 -112 TTGGTCGGTGTTTCTGTGGCGGAATTAGTG 2 213 1 TTTCTGTGGC 0.982183 -88 AAAGCACCTTTGAATGGTGCTTTTATTTT 2 282 1 TGAATGGTGC 0.954313 -19 ********** Masking position 5 Map Score: 8.34673 Number of sites scoring better than the average of aligned sites = 612 Number in coding regions = 553 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 AACTAAGATTGGCGCAGGAATACCTAAACCA 2 23 0 GGCGCAGGAT 0.980863 -278 ATACGCATAAGTTGCAGGCATTAAACCAACT 2 50 0 GTTGCAGGAT 0.979327 -251 ACAGTTTTATGGTGCCAGGTTTAATTGGGGT 2 169 1 GGTGCCAGTT 0.958615 -132 TGGGGTTGTTGTTGCTTGCTTGGTCGGTGTT 2 194 1 GTTGCTTGTT 0.971194 -107 ACCATTCAAAGGTGCTTTTATATTAAAAGGA 2 269 0 GGTGCTTTAT 0.984352 -32 ACCTTTGAATGGTGCTTTTATTTT 2 287 1 GGTGCTTTAT 0.984352 -14 ******** ** Masking position 11 Map Score: 3.96022 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 156 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TTTTAGGCAATAAAAAATCCTTGATTTTAT 1 27 0 TAAAAAATCC 0.917991 -83 AATTCCGCCACAGAAACACCGACCAAGCAA 2 209 0 CAGAAACACC 0.974789 -92 CCTTTTAATATAAAAGCACCTTTGAATGGT 2 270 1 TAAAAGCACC 0.99428 -31 AAAATAAAAGCACCATTCAAAGGT 2 287 0 TAAAAGCACC 0.99428 -14 ********** Masking position 5 Map Score: 2.45371 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 54 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 TCAAAAAAATCCTTATATAAAA 1 3 1 AAAAAAATCC 0.966148 -107 TTTTAGGCAATAAAAAATCCTTGATTTTAT 1 27 0 TAAAAAATCC 0.875639 -83 GGAATACCTAAACCAATACCAACAGGT 2 8 0 AACCAATACC 0.906727 -293 ACAACAACCCCAATTAAACCTGGCACCATA 2 176 0 CAATTAAACC 0.817569 -125 CCAAGCAAGCAACAACAACCCCAATTAAAC 2 187 0 AACAACAACC 0.923218 -114 ATTAGCGAATCACTAATTCCGCCACAGAAA 2 223 0 CACTAATTCC 0.935572 -78 TTTACACACAAACTAAATCCTTTTAATATA 2 252 1 AACTAAATCC 0.983318 -49 AAAATAAAAGCACCATTCAAA 2 290 0 AAATAAAAGC 0.860156 -11 ********** Masking position 2 Map Score: 4.1963 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 509 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 ********** No masking Map Score: 3.15071e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: 3.15071e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 3.15071e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0