AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -icoldbox_mjan_opreg_300.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0669 59 ATP-dependent RNA helicase, DEAD-family (deaD) #2 MJ0671 56 riboflavin-specific deaminase (ribG) #3 MJ0672 263 membrane bound transport protein, putative Motif number 1 TAGCATCTTTAAAAATTAAATTTTA 1 45 1 AAAAATTAAA 0.98745 -15 TTTAGAATATAAAACTTAAATTTTATTAAC 2 24 1 AAAACTTAAA 0.984825 -33 TTATTAACTAAACATTTAAAA 2 46 1 AACATTTAAA 0.884399 -11 TCCAGTTAAAAAATATTAAAAACAATTATT 3 23 0 AAATATTAAA 0.969078 -241 ATAAAATAATAAGAAAGAAATCCAGTTAAA 3 43 0 AAGAAAGAAA 0.8615 -221 AAAGGCATGGAAATAATAAAATAATAAGAA 3 58 0 AAATAATAAA 0.94866 -206 AACTTAAAGTAAAAATTATAGAATTTATGA 3 110 0 AAAAATTATA 0.909059 -154 TTTACAAAACAAAACTTAAAGTAAAAATTA 3 122 0 AAAACTTAAA 0.984825 -142 AAGAGATATAAAAACTTAACTATTAACATA 3 201 1 AAAACTTAAC 0.924367 -63 TAACATACCTAAGTTATAAAGTAAAGAAAT 3 224 1 AAGTTATAAA 0.828071 -40 TTATAAAGTAAAGAAATAAATCTGGTGGGG 3 237 1 AAGAAATAAA 0.970614 -27 ********** Masking position 8 Map Score: 17.0178 Number of sites scoring better than the average of aligned sites = 1562 Number in coding regions = 1143 Number in noncoding regions = 419 Number of orfs with sites within 600 bp upstream = 331 Fraction of orfs with sites within 600 bp upstream = 0.0531642 Motif number 2 TAGTTGTTGAGGATGCTAAAATCTCTTTTTA 1 16 1 GGATGCAAAA 0.848502 -44 TAATTTTTAAAGATGCTAAAAAGAGATTTTA 1 32 0 AGATGCAAAA 0.9641 -28 GCTATCATTTAGAATATAAAACTTAAATTTT 2 17 1 AGAATAAAAA 0.890751 -40 TTAAATGTTTAGTTAATAAAATTTAAGTTTT 2 34 0 AGTTAAAAAA 0.978425 -23 AAAGAAATCCAGTTAAAAAATATTAAAAACA 3 29 0 AGTTAAAAAT 0.926379 -235 AAAGGCATGGAAATAATAAAATAATAAGAAA 3 57 0 AAATAAAAAA 0.88149 -207 TTTGGAATAAACTAACCAAAAGGCATGGAAA 3 75 0 ACTAACAAAA 0.886461 -189 TGTCTCTTTTACAAAACAAAACTTAAAGTAA 3 128 0 ACAAAAAAAA 0.932696 -136 AACATACAAGAGATATAAAAACTTAACTATT 3 194 1 AGATATAAAA 0.932561 -70 TAAGTTATAAAGTAAAGAAATAAATCTGGTG 3 233 1 AGTAAAAAAT 0.896248 -31 ****** **** Masking position 8 Map Score: 7.21073 Number of sites scoring better than the average of aligned sites = 1994 Number in coding regions = 1744 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 3 CTTAAATTTTATTAACTAAACATTTAAAA 2 38 1 ATTAACTAAA 0.954244 -19 AGTATTTGGAATAAACTAACCAAAAGGCAT 3 80 0 ATAAACTAAC 0.983808 -184 TGAATAATGAATAAACATACAAGAGATATA 3 181 1 ATAAACATAC 0.970501 -83 CAAGAGATATAAAAACTTAACTATTAACAT 3 200 1 AAAAACTTAA 0.905965 -64 AAACTTAACTATTAACATACCTAAGTTATA 3 212 1 ATTAACATAC 0.946344 -52 TACCTAAGTTATAAAGTAAAGAAATAAATC 3 229 1 ATAAAGTAAA 0.899399 -35 ********** Masking position 5 Map Score: 4.98118 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 363 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 4 AGGATGCTAAAATCTCTTTTTAGCATCTTT 1 25 1 AATCTCTTTT 0.978883 -35 GCCTGACCCGTGTCTCTTTTACAAAACAAA 3 139 0 TGTCTCTTTT 0.985656 -125 TAAGTTTTTATATCTCTTGTATGTTTATTC 3 189 0 TATCTCTTGT 0.985656 -75 CCACCAGATTTATTTCTTTACTTTATAACT 3 235 0 TATTTCTTTA 0.921065 -29 ********** Masking position 5 Map Score: 1.78698 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 233 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 AAGAGATTTTAGCATCCTCAACAACTATGGGC 1 9 0 ACATCCAAAA 0.980641 -51 ATCTCTTTTTAGCATCTTTAAAAATTAAATTTTA 1 36 1 ACATCTAAAA 0.991184 -24 AATTTAGCTATCATTTAGAATATAAAACTTAAA 2 10 1 ACATTTAAAT 0.943504 -47 ATTAACACCTGTAATAATTGTTTTTAA 3 4 1 ACACCTAAAA 0.976256 -260 CCAGTTAAAAAATATTAAAAACAATTATTACAGG 3 18 0 ATATTAAAAA 0.880158 -246 GAATTTATGAAGTATTTGGAATAAACTAACCAAA 3 86 0 ATATTTAAAA 0.960258 -178 * ***** ** ** Masking position 10 Map Score: 1.4796 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 330 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 ********** No masking Map Score: 1.65857e-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: 1.65857e-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: 1.65857e-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