AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i307_mjan_pyro_300.orf -o307_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -x5 -e 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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ00828 300 M_jannaschii_chromosome #2 RMJ01433 174 M_jannaschii_chromosome #3 RMJ13076 300 M_jannaschii_chromosome #4 RMJ05639 152 M_jannaschii_chromosome #5 RPH01428 22 Pyrococcus_OT3 #6 RPH01431 27 Pyrococcus_OT3 #7 RPH01432 156 Pyrococcus_OT3 #8 RPH01767 57 Pyrococcus_OT3 Motif number 1 TTATTAATTTAAATTAATAAATATTATTACC 1 96 0 AATTAATAAA 0.907835 -205 TTATTAATTTAAATTAATAAAGATTACAATT 1 107 1 AATTAATAAA 0.907835 -194 AATAAAGATTACAATTTTAAAAACGAAATTT 1 122 1 AAATTTTAAA 0.971102 -179 TTTAAAAACGAAATTTTTAAATATTTTTAAA 1 137 1 AATTTTTAAA 0.961075 -164 AGATTATTTGAAAATTTTAAAAATATTTAAA 1 152 0 AAATTTTAAA 0.971101 -149 CTTTTTTAATATAAGTTTAAATATTTAGAAG 1 181 1 AAAGTTTAAA 0.874001 -120 ATTTAGAAGCATAATTATAATTTCATTTTTT 1 203 1 AAATTATAAT 0.806859 -98 ATATCAATAAAATTTTCTAAATCTTTGGTAG 1 276 0 ATTTTCTAAA 0.709392 -25 AGGAAAAATTATATACTAAAAAATC 2 5 1 AAATTATATA 0.817642 -170 TATATACTAAAAAATCTTAAATAGATTATGC 2 20 1 AAATCTTAAA 0.830565 -155 AATAAGGTATATTTTTATAAAGAGAGTGTCT 2 116 0 ATTTTATAAA 0.921091 -59 GAGATATAGGATTATAATAAAAGTGGTGATA 3 98 0 ATATAATAAA 0.836582 -203 AATAAAAAAGAAAAGAATAAAAATAATAAGA 3 195 1 AAAGAATAAA 0.73455 -106 CACCATTATAAGTATTTTAAAGTAGTTAAAT 3 267 0 ATATTTTAAA 0.940933 -34 ATTATAGTAAAATTTTTAAATCCAACTATT 4 10 1 AATTTTTAAA 0.961075 -143 TTTAAATCCAACTATTTTAAATTATTTTTAG 4 25 1 ATATTTTAAA 0.940933 -128 ATACTCCCAAATAATATTAATACTCTAAAAA 4 49 0 AAATATTAAT 0.641064 -104 CACTAAAGTAATTTTTATAAATTCAAAACCC 4 92 1 ATTTTATAAA 0.921091 -61 CTTAGCCGAAACATTTATATAATGTGGGGAG 4 122 1 AATTTATATA 0.767167 -31 * ********* Masking position 8 Map Score: 22.2483 Number of sites scoring better than the average of aligned sites = 1872 Number in coding regions = 1302 Number in noncoding regions = 570 Number of orfs with sites within 600 bp upstream = 447 Fraction of orfs with sites within 600 bp upstream = 0.0717957 Motif number 2 CCCTGCACCATTTTTATTTTAGGTAATAATA 1 75 1 TTTTTTTTTA 0.665409 -226 ATATTTAAAAATTTCGTTTTTAAAATTGTAA 1 130 0 ATTTCTTTTT 0.922783 -171 ACGAAATTTTTAAATATTTTTAAAATTTTCA 1 144 1 TAAATTTTTT 0.577405 -157 AATTTTCAAATAATCTTTTTTAATATAAGTT 1 167 1 TAATCTTTTT 0.8912 -134 CATAATTATAATTTCATTTTTTAGGTGATGA 1 212 1 ATTTCTTTTT 0.922783 -89 ATTTTTTAGTATATAATTTTTCCT 2 4 0 ATATATTTTT 0.648912 -171 TTCTTTTTTATTTTTATTTTTATAGTCTTAT 3 176 0 TTTTTTTTTT 0.944964 -125 ATTTTTATTCTTTTCTTTTTTATTTTTATTT 3 188 0 TTTTCTTTTT 0.958405 -113 TTATAATATCTTATTATTTTTATTCTTTTCT 3 203 0 TTATTTTTTT 0.944963 -98 AATAATTAGCTTAATGTTTTTAACTAATTCA 3 239 0 TTAATTTTTT 0.793677 -62 CAACTATTTTAAATTATTTTTAGAGTATTAA 4 33 1 AAATTTTTTT 0.759895 -120 ATTTTTCCTTTTTGTGGGGGTGA 6 3 1 TTTTCTTTTT 0.958405 -25 ***** ***** Masking position 7 Map Score: 10.2051 Number of sites scoring better than the average of aligned sites = 1196 Number in coding regions = 844 Number in noncoding regions = 352 Number of orfs with sites within 600 bp upstream = 269 Fraction of orfs with sites within 600 bp upstream = 0.0432059 Motif number 3 ATAATTTCATTTTTTAGGTGATGAGATTGGAGA 1 219 1 TTTAGGGATG 0.945188 -82 ATTTAGAAAATTTTATTGATATGTAT 1 285 1 TTTTTGTATG 0.706336 -16 TAGAGGGTGTTAAACTGGGGAGACACTCTCTTT 2 96 1 TAATGGGAGA 0.78463 -79 GGATTATAATAAAAGTGGTGATATGGAATGAAG 3 88 0 AAATGGGATA 0.599272 -213 CCATAAATTATATATATGAGATATAGGATTATA 3 113 0 TATATGGATA 0.446369 -188 CATATATATAATTTATGGTTATGTCAATACTTA 3 128 1 ATTTGGTATG 0.714961 -173 TAGTCTTATTTTATATGGTTGTGTTAAGTATTG 3 152 0 TTATGGTGTG 0.913986 -149 TAATAAGATATTATAATGAGATGAATTAGTTAA 3 218 1 TTAATGGATG 0.660453 -83 TTAAAATACTTATAATGGTGATATTTTATGCAA 3 278 1 TATTGGGATA 0.927058 -23 AACATTTATATAATGTGGGGAGGGATATTATG 4 131 1 TAATGGGAGG 0.9194 -22 ATTTTTCCTTTTTGTGGGGGTGAAACC 6 10 1 TTTTGGGGTG 0.980035 -18 AACGTTGAACTTTAATGGCGGTGATGGGCC 7 8 0 TTTTGGGGTG 0.980035 -149 TTGACTTACTTAAGGTGGAGGTGAGAAG 7 139 1 TAATGGGGTG 0.966961 -18 ACCATAACTGTTTTTAGGCTGTAGTAATAAATT 8 26 0 TTTAGGTGTA 0.656143 -32 TAAAAACAGTTATGGTGGTTGGGGT 8 43 1 TATTGGTGGG 0.853611 -15 *** *** **** Masking position 8 Map Score: 10.3249 Number of sites scoring better than the average of aligned sites = 1110 Number in coding regions = 944 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 4 ATTTTAGGTAATAATATTTATTAATTTAAA 1 90 1 ATAATATTTA 0.665152 -211 GAAAATTTTAAAAATATTTAAAAATTTCGT 1 144 0 AAAATATTTA 0.730288 -157 AAGATTATTTGAAAATTTTAAAAATATTTA 1 154 0 GAAAATTTTA 0.365618 -147 TAAAATTTTCAAATAATCTTTTTTAATATA 1 164 1 AAATAATCTT 0.614646 -137 ATCTTTTTTAATATAAGTTTAAATATTTAG 1 179 1 ATATAAGTTT 0.501473 -122 ATACATATCAATAAAATTTTCTAAATCTTT 1 281 0 ATAAAATTTT 0.89267 -20 ATTTTTTAGTATATAATTTTTCCT 2 5 0 ATATAATTTT 0.820137 -170 ATTATATACTAAAAAATCTTAAATAGATTA 2 18 1 AAAAAATCTT 0.768316 -157 AGTTCTTTGCAAAACATTTTAGAATAAATA 2 143 0 AAAACATTTT 0.875235 -32 TATCTCATATATATAATTTATGGTTATGTC 3 123 1 ATATAATTTA 0.835642 -178 GAATTAGTTAAAAACATTAAGCTAATTATT 3 240 1 AAAACATTAA 0.470317 -61 ATTATAGTAAAATTTTTAAATCCAAC 4 7 1 GTAAAATTTT 0.811782 -146 AATACTCTAAAAATAATTTAAAATAGTTGG 4 32 0 AAATAATTTA 0.895114 -121 TTTTGAATTTATAAAAATTACTTTAGTGAG 4 90 0 ATAAAAATTA 0.462733 -63 ACCCTTAGCCGAAACATTTATATAATGTGG 4 119 1 GAAACATTTA 0.847256 -34 TGAGATCATGGAAACATTTTAATATCAATG 7 54 0 GAAACATTTT 0.832179 -103 GCGAGAGCACAAATAATTTTAGCCTATTAG 7 91 0 AAATAATTTT 0.870475 -66 CGACCTCAGTAAAAAATTTATTACTACAGC 8 12 1 AAAAAATTTA 0.943378 -46 CTACAGCCTAAAAACAGTTATGGTGGTTGG 8 35 1 AAAACAGTTA 0.731315 -23 ********** Masking position 3 Map Score: 13.7189 Number of sites scoring better than the average of aligned sites = 2200 Number in coding regions = 1560 Number in noncoding regions = 640 Number of orfs with sites within 600 bp upstream = 469 Fraction of orfs with sites within 600 bp upstream = 0.0753293 Motif number 5 CCGAACCCCTACGGGACCGGATCTTAAGTCC 1 28 0 AGGGACCGGA 0.979473 -273 CCGGTCCCGTAGGGGTTCGGGGGTTCAAATC 1 39 1 AGGGTTCGGG 0.955173 -262 GGTGCAGGGGAGGGGATTTGAACCCCCGAAC 1 53 0 AGGGATTTGA 0.97812 -248 TTTTTAGGTGATGAGATTGGAGAAAGTTTTC 1 229 1 AGAGATTGGA 0.959599 -72 TGTTTCGGCTAAGGGTTTTGAATTTATAAAA 4 104 0 AGGGTTTTGA 0.97812 -49 GAAGGTATATAAGAGTCTTGACTTACTTAAG 7 122 1 AGAGTCTTGA 0.926048 -35 * ********* Masking position 1 Map Score: 1.54913 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 49 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 AATAAATATTATTACCTAAAATAAAAATGG 1 82 0 ATTACCTAAA 0.882082 -219 CTTTTTTAATATAAGTTTAAATATTTAGAA 1 181 1 ATAAGTTTAA 0.837523 -120 CTCCAATCTCATCACCTAAAAAATGAAATT 1 221 0 ATCACCTAAA 0.733937 -80 TGGTAGTAGGATTGGTTAGATAGAAAACTT 1 252 0 ATTGGTTAGA 0.672166 -49 TTCATCTTAGATAAGTTAAAGAAAGCTAAT 3 28 0 ATAAGTTAAA 0.948716 -273 AATGAGATGAATTAGTTAAAAACATTAAGC 3 232 1 ATTAGTTAAA 0.957531 -69 TAGTTAAATAATTAGCTTAATGTTTTTAAC 3 246 0 ATTAGCTTAA 0.857917 -55 AGTATTTTAAAGTAGTTAAATAATTAGCTT 3 258 0 AGTAGTTAAA 0.826626 -43 TACTCTAAAAATAATTTAAAATAGTTGGAT 4 30 0 ATAATTTAAA 0.674522 -123 ACCATACCTAATAGGCTAAAATTATTTGTG 7 84 1 ATAGGCTAAA 0.896158 -73 ********** Masking position 7 Map Score: 4.35682 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 402 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 ********** No masking Map Score: -6.86794e-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: -6.86794e-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 9 ********** No masking Map Score: -6.86794e-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