AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -icoldbox_mjan_opreg_100.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 0.987394 -15 TTTAGAATATAAAACTTAAATTTTATTAAC 2 24 1 AAAACTTAAA 0.984758 -33 TTATTAACTAAACATTTAAAA 2 46 1 AACATTTAAA 0.88394 -11 TCCAGTTAAAAAATATTAAAAACAATTATT 3 23 0 AAATATTAAA 0.968943 -241 ATAAAATAATAAGAAAGAAATCCAGTTAAA 3 43 0 AAGAAAGAAA 0.860964 -221 AAAGGCATGGAAATAATAAAATAATAAGAA 3 58 0 AAATAATAAA 0.948441 -206 AACTTAAAGTAAAAATTATAGAATTTATGA 3 110 0 AAAAATTATA 0.908688 -154 TTTACAAAACAAAACTTAAAGTAAAAATTA 3 122 0 AAAACTTAAA 0.984758 -142 AAGAGATATAAAAACTTAACTATTAACATA 3 201 1 AAAACTTAAC 0.924053 -63 TAACATACCTAAGTTATAAAGTAAAGAAAT 3 224 1 AAGTTATAAA 0.827431 -40 TTATAAAGTAAAGAAATAAATCTGGTGGGG 3 237 1 AAGAAATAAA 0.970486 -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 TAAAATTTAATTTTTAAAGATGCTAAAAA 1 41 0 AATTTTTAAG 0.984171 -19 AATAAAATTTAAGTTTTATATTCTAAATGAT 2 20 0 AAGTTTTAAT 0.975514 -37 TTTTAAATGTTTAGTTAATAAAATTT 2 41 0 AATGTTTATT 0.855799 -16 TATTAAAAACAATTATTACAGGTGTTAAT 3 9 0 AATTATTAAG 0.906521 -255 AAAATTATAGAATTTATGAAGTATTTGGAAT 3 98 0 AATTTATGAG 0.90597 -166 TAAATTCTATAATTTTTACTTTAAGTTTTGT 3 113 1 AATTTTTATT 0.930902 -151 TTTTTACTTTAAGTTTTGTTTTGTAAAAGAG 3 125 1 AAGTTTTGTT 0.911021 -139 TTAATAGTTAAGTTTTTATATCTCTTGTATG 3 196 0 AGTTTTTAAT 0.918829 -68 TAACATACCTAAGTTATAAAGTAAAGAAATA 3 224 1 AAGTTATAAG 0.941905 -40 ******** ** Masking position 7 Map Score: 8.5512 Number of sites scoring better than the average of aligned sites = 927 Number in coding regions = 685 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 3 AAAAAGAGATTTTAGCATCCTCAACAACTA 1 16 0 TTTAGCATCC 0.987057 -44 AAAATCTCTTTTTAGCATCTTTAAAAATTA 1 33 1 TTTAGCATCT 0.979794 -27 TTAGCTATCATTTAGAATATAAAACTTAAA 2 14 1 TTTAGAATAT 0.826738 -43 ATTAACACCTGTAATAATTG 3 1 1 ATTAACACCT 0.918555 -263 TGAATAATGAATAAACATACAAGAGATATA 3 181 1 ATAAACATAC 0.883795 -83 AAACTTAACTATTAACATACCTAAGTTATA 3 212 1 ATTAACATAC 0.968594 -52 ********** Masking position 4 Map Score: 3.08036 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 407 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 GGATGCTAAAATCTCTTTTTAGCATCTTTA 1 26 1 ATCTCTTTTT 0.964828 -34 ATTGTTTTTAATATTTTTTAACTGGATTTC 3 27 1 ATATTTTTTA 0.946748 -237 CATAAATTCTATAATTTTTACTTTAAGTTT 3 111 1 ATAATTTTTA 0.843838 -153 CCTGACCCGTGTCTCTTTTACAAAACAAAA 3 138 0 GTCTCTTTTA 0.975995 -126 AAGTTTTTATATCTCTTGTATGTTTATTCA 3 188 0 ATCTCTTGTA 0.975995 -76 ********** Masking position 6 Map Score: 2.09522 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 539 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 5 ********** 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 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